DNA in bacterial chromosomes is organized into higher-order structures by DNA-binding proteins called nucleoid-associated proteins (NAPs) or bacterial chromatin proteins (BCPs). BCPs often bind to or near DNA loci transcribed by RNA polymerase (RNAP) and can either increase or decrease gene expression. To understand the mechanisms by which BCPs alter transcription, one must consider both steric effects and the topological forces that arise when DNA deviates from its fully relaxed double-helical structure. Transcribing RNAP creates DNA negative (−) supercoils upstream and positive (+) supercoils downstream whenever RNAP and DNA are unable to rotate freely. This (−) and (+) supercoiling generates topological forces that resist forward translocation of DNA through RNAP unless the supercoiling is constrained by BCPs or relieved by topoisomerases. BCPs also may enhance topological stress and overall can either inhibit or aid transcription. Here, we review current understanding of how RNAP, BCPs, and DNA topology interplay to control gene expression.

中文翻译：

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细菌染色质蛋白、转录和 DNA 拓扑：基因表达控制中不可分割的伙伴


细菌染色体中的 DNA 通过称为类核相关蛋白 (NAP) 或细菌染色质蛋白 (BCP) 的 DNA 结合蛋白组织成更高级的结构。 BCP 通常与 RNA 聚合酶 (RNAP) 转录的 DNA 位点结合或附近，并且可以增加或减少基因表达。为了理解 BCP 改变转录的机制，我们必须考虑空间效应和 DNA 偏离其完全松弛的双螺旋结构时产生的拓扑力。当 RNAP 和 DNA 无法自由旋转时，转录 RNAP 会在上游产生 DNA 负 (-) 超螺旋，在下游产生正 (+) 超螺旋。这种 (-) 和 (+) 超螺旋产生拓扑力，阻止 DNA 通过 RNAP 向前易位，除非超螺旋受到 BCP 限制或被拓扑异构酶缓解。 BCP 还可能增强拓扑应力，总体上可以抑制或帮助转录。在这里，我们回顾了目前对 RNAP、BCP 和 DNA 拓扑如何相互作用来控制基因表达的理解。