Antipov S S, Tutukina M N, Preobrazhenskaya E V, Kondrashov F A, Patrushev M V, Toshchakov S V, Dominova I, Shvyreva U S, Vrublevskaya V V, Morenkov O S, Sukharicheva N A, Panyukov V V, Ozoline O N
Department of Functional Genomics and Cellular Stress, Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
Department of Cell Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation.
PLoS One. 2017 Aug 11;12(8):e0182800. doi: 10.1371/journal.pone.0182800. eCollection 2017.
Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity. However, deletion of dps changed the profile of proteins in starved cells, SELEX screen revealed genomic regions preferentially bound in vitro and certain affinity of Dps for artificial branched molecules was detected by atomic force microscopy. Here we report a non-random distribution of Dps binding sites across the bacterial chromosome in exponentially growing cells and show their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. In the dps-null mutant we, therefore, observed a differentially altered expression of several targeted genes and found suppressed transcription from the dps promoter. In most cases this can be explained by the relieved interference with Dps for nucleoid proteins exploiting sequence-specific modes of DNA binding. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA polymerase or, vice versa, competing with inhibitors to activate transcription.
Dps是一种多功能的同型十二聚体蛋白，它能氧化Fe2+离子，并将其以Fe2O3的形式积累在其蛋白腔内，在饥饿时与DNA紧密相互作用使细菌类核浓缩，还具有其他一些功能。自该蛋白被发现后的二十年里，其铁氧化酶活性已得到相当深入的研究，但Dps与DNA相互作用的机制仍然成谜。赖氨酸残基在无结构的N端尾巴中的关键作用导致了一种传统观点，即Dps结合DNA时没有序列或结构特异性。然而，dps的缺失改变了饥饿细胞中的蛋白质谱，SELEX筛选揭示了体外优先结合的基因组区域，并且通过原子力显微镜检测到Dps对人工分支分子具有一定亲和力。在这里，我们报告了在指数生长的细胞中Dps结合位点在细菌染色体上的非随机分布，并表明它们富含易于形成二级结构的反向重复序列。我们发现Dps结合区域与其他类核蛋白占据的位点重叠，并且包含其共有序列中典型的过度代表基序。在两种具有广泛蛋白质占据的基因组结构域中，一种可能是高表达的，另一种可能是转录沉默的，只有那些富含RNA聚合酶分子的结构域优先被Dps占据。因此，在dps缺失突变体中，我们观察到几个靶向基因的表达有差异改变，并发现dps启动子的转录受到抑制。在大多数情况下，这可以通过Dps对利用序列特异性DNA结合模式的类核蛋白的干扰减轻来解释。因此，在指数生长期间保护细菌细胞免受不同压力时，Dps可以通过与RNA聚合酶竞争来调节细菌染色体的转录完整性，从而阻碍某些基因的RNA生物合成，或者反之，与抑制剂竞争以激活转录。
