Melekhov Vladislav V, Shvyreva Uliana S, Timchenko Alexander A, Tutukina Maria N, Preobrazhenskaya Elena V, Burkova Diana V, Artiukhov Valiriy G, Ozoline Olga N, Antipov Sergey S
Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation; Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
PLoS One. 2015 May 15;10(5):e0126504. doi: 10.1371/journal.pone.0126504. eCollection 2015.
Multifunctional protein Dps plays an important role in iron assimilation and a crucial role in bacterial genome packaging. Its monomers form dodecameric spherical particles accumulating ~400 molecules of oxidized iron ions within the protein cavity and applying a flexible N-terminal ends of each subunit for interaction with DNA. Deposition of iron is a well-studied process by which cells remove toxic Fe2+ ions from the genetic material and store them in an easily accessible form. However, the mode of interaction with linear DNA remained mysterious and binary complexes with Dps have not been characterized so far. It is widely believed that Dps binds DNA without any sequence or structural preferences but several lines of evidence have demonstrated its ability to differentiate gene expression, which assumes certain specificity. Here we show that Dps has a different affinity for the two DNA fragments taken from the dps gene regulatory region. We found by atomic force microscopy that Dps predominantly occupies thermodynamically unstable ends of linear double-stranded DNA fragments and has high affinity to the central part of the branched DNA molecule self-assembled from three single-stranded oligonucleotides. It was proposed that Dps prefers binding to those regions in DNA that provide more contact pads for the triad of its DNA-binding bundle associated with one vertex of the protein globule. To our knowledge, this is the first study revealed the nucleoid protein with an affinity to branched DNA typical for genomic regions with direct and inverted repeats. As a ubiquitous feature of bacterial and eukaryotic genomes, such structural elements should be of particular care, but the protein system evolutionarily adapted for this function is not yet known, and we suggest Dps as a putative component of this system.
多功能蛋白Dps在铁同化过程中发挥着重要作用，在细菌基因组包装中也起着关键作用。其单体形成十二聚体球形颗粒，在蛋白腔内积累约400个氧化铁离子分子，并利用每个亚基灵活的N末端与DNA相互作用。铁的沉积是一个经过充分研究的过程，通过这个过程细胞从遗传物质中去除有毒的Fe2+离子，并以易于获取的形式储存它们。然而，与线性DNA的相互作用模式仍然神秘，到目前为止，与Dps的二元复合物尚未得到表征。人们普遍认为Dps结合DNA时没有任何序列或结构偏好，但有几条证据表明它具有区分基因表达的能力，这意味着它具有一定的特异性。在这里，我们表明Dps对取自dps基因调控区的两个DNA片段具有不同的亲和力。我们通过原子力显微镜发现，Dps主要占据线性双链DNA片段热力学不稳定的末端，并且对由三个单链寡核苷酸自组装而成的分支DNA分子的中心部分具有高亲和力。有人提出，Dps更喜欢结合DNA中那些为与其蛋白球体一个顶点相关的DNA结合束三联体提供更多接触位点的区域。据我们所知，这是第一项揭示对具有直接和反向重复的基因组区域典型的分支DNA具有亲和力的类核蛋白的研究。作为细菌和真核生物基因组的普遍特征，这样的结构元件应该受到特别关注，但尚未发现进化上适应此功能的蛋白质系统，我们建议Dps作为该系统的一个假定组成部分。
