Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Microbial Biochemistry, Pawinskiego 5a, 02-106 Warsaw, Poland.
Nucleic Acids Res. 2018 May 18;46(9):4592-4606. doi: 10.1093/nar/gky257.
ParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in the separation of ori domains by binding to parS palindromes, mainly localized close to oriC. In Pseudomonas aeruginosa neither ParB deficiency nor modification of all 10 parSs is lethal. However, such mutants show not only defects in chromosome segregation but also growth retardation and motility dysfunctions. Moreover, a lack of parB alters expression of over 1000 genes, suggesting that ParB could interact with the chromosome outside its canonical parS targets. Here, we show that indeed ParB binds specifically to hundreds of sites in the genome. ChIP-seq analysis revealed 420 ParB-associated regions in wild-type strain and around 1000 in a ParB-overproducing strain and in various parS mutants. The vast majority of the ParB-enriched loci contained a heptanucleotide motif corresponding to one arm of the parS palindrome. All previously postulated parSs, except parS5, interacted with ParB in vivo. Whereas the ParB binding to the four parS sites closest to oriC, parS1-4, is involved in chromosome segregation, its genome-wide interactions with hundreds of parS half-sites could affect chromosome topology, compaction and gene expression, thus allowing P. aeruginosa ParB to be classified as a nucleoid-associated protein.
ParA 和 ParB 同源物参与细菌中染色体的准确分离。ParB 通过与 parS 回文结合参与 ori 域的分离，主要定位于 oriC 附近。在铜绿假单胞菌中，ParB 缺乏或修饰所有 10 个 parSs 都不会致命。然而，这些突变体不仅表现出染色体分离缺陷，而且还表现出生长迟缓和运动功能障碍。此外，缺乏 parB 会改变超过 1000 个基因的表达，表明 ParB 可以与染色体在其典型的 parS 靶标之外相互作用。在这里，我们表明 ParB 确实可以特异性地结合基因组中的数百个位点。ChIP-seq 分析显示，在野生型菌株中有 420 个 ParB 相关区域，在 ParB 过表达菌株和各种 parS 突变体中有近 1000 个。ParB 富集的绝大多数基因座都包含一个七核苷酸基序，对应于 parS 回文的一条臂。所有以前假定的 parSs，除了 parS5 之外，都与体内的 ParB 相互作用。尽管 ParB 与 oriC 最接近的四个 parS 位点（parS1-4）的结合参与了染色体分离，但它与数百个 parS 半位点的全基因组相互作用可能会影响染色体拓扑结构、压缩和基因表达，从而使铜绿假单胞菌 ParB 被归类为核相关蛋白。
