Pseudomonas aeruginosa partitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of a parS-related motif

Abstract

ABSTRACTParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in separation of ori domains by binding to specific parS sites, mainly localized close to oriC. In Pseudomonas aeruginosa neither a lack of parB gene nor modification of ten parSs is lethal. Remarkably, 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 one thousand genes, suggesting that ParB could interact with the chromosome outside its canonical parS targets.Indeed, DNA immunoprecipitation with anti-ParB antibodies followed by deep sequencing (ChIP-seq) revealed 420 enriched regions in WT PAO1161 strain and around 1000 in a ParB-overproducing strain and in various parS mutants. Vast majority of the ParB-enriched loci contained a heptanucleotide motif corresponding to one arm of the parS palindrome. All previously postulated parS sites with the exception of 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 classifying P. aeruginosa ParB as a Nucleoid Associated Protein (NAP).