H-NS-like proteins in Pseudomonas aeruginosa coordinately silence intragenic transcription [ChIP-seq]

The H-NS-like proteins MvaT and MvaU act coordinately as global repressors in Pseudomonas aeruginosa by binding to AT-rich regions of the chromosome. Although cells can tolerate the loss of either protein, identifying their combined regulatory effects has been challenging because the loss of both proteins is lethal due to induction of prophage Pf4 and subsequent superinfection of the cell. In other bacteria, H-NS promotes cellular fitness by inhibiting intragenic transcription from AT-rich target regions, preventing them from sequestering RNA polymerase; however, it is not known if whether MvaT and MvaU function similarly. Here we utilize a parental strain that cannot be infected by Pf4 phage to define the collective MvaT and MvaU regulon and demonstrate that the combined loss of both MvaT and MvaU leads to increased intragenic transcription from loci directly controlled by these proteins. We further show that the loss of MvaT and MvaU leads to a striking redistribution of RNA polymerase containing σ70 to genomic regions vacated by these proteins. Our findings suggest that the ability of H-NS-like proteins to repress intragenic transcription is a universal function of these proteins and point to a second mechanism by which MvaT and MvaU may contribute to the growth of P. aeruginosa. Genome-wide locations of RpoD in a parental strain lacking pilY1 and a strain with additional deletions of mvaU and mvaT. Also, genome-wide locations of MvaT and MvaU in wild-type cells.

类H-NS蛋白（H-NS-like proteins）MvaT与MvaU可通过结合铜绿假单胞菌（Pseudomonas aeruginosa）染色体的AT富集区域，协同发挥全局阻遏因子的功能。尽管单株细胞可耐受其中一种蛋白的缺失，但解析二者的联合调控效应颇具挑战——因为同时缺失两种蛋白会因原噬菌体Pf4（prophage Pf4）的诱导以及后续的细胞超感染而致死。在其他细菌中，H-NS蛋白可通过抑制AT富集靶区域的基因内转录，避免这些区域竞争结合RNA聚合酶（RNA polymerase），从而提升细胞适应性；但目前尚不清楚MvaT与MvaU是否具备类似功能。本研究利用一株无法被Pf4噬菌体感染的亲本菌株，明确了MvaT与MvaU的联合调控组，并证实同时缺失二者会导致这些蛋白直接调控的基因座出现增强的基因内转录。我们进一步发现，MvaT与MvaU的缺失会使携带σ⁷⁰的RNA聚合酶发生显著的基因组重分布，转移至这些蛋白空出的基因组区域。本研究结果表明，类H-NS蛋白阻遏基因内转录的能力是这类蛋白的通用功能，并揭示了MvaT与MvaU促进铜绿假单胞菌生长的第二种潜在机制。本数据集包含：缺失pilY1的亲本菌株，以及额外缺失mvaU与mvaT的菌株中RpoD的全基因组结合位点；同时还包含野生型菌株中MvaT与MvaU的全基因组结合位点。