Permissive zones for the centromere-binding protein ParB on the Caulobacter crescentus chromosome

• Published in: Nucleic acids research 2018-02, Vol.46 (3), p.1196-1209
• Main Authors: Tran, Ngat T, Stevenson, Clare E, Som, Nicolle F, Thanapipatsiri, Anyarat, Jalal, Adam S B, Le, Tung B K
• Format: Article
• Language: English
• Subjects: Gene regulation, Chromatin and Epigenetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkx1192

Abstract Proper chromosome segregation is essential in all living organisms. In Caulobacter crescentus, the ParA-ParB-parS system is required for proper chromosome segregation and cell viability. The bacterial centromere-like parS DNA locus is the first to be segregated following chromosome replication. parS is bound by ParB protein, which in turn interacts with ParA to partition the ParB-parS nucleoprotein complex to each daughter cell. Here, we investigated the genome-wide distribution of ParB on the Caulobacter chromosome using a combination of in vivo chromatin immunoprecipitation (ChIP-seq) and in vitro DNA affinity purification with deep sequencing (IDAP-seq). We confirmed two previously identified parS sites and discovered at least three more sites that cluster ∼8 kb from the origin of replication. We showed that Caulobacter ParB nucleates at parS sites and associates non-specifically with ∼10 kb flanking DNA to form a high-order nucleoprotein complex on the left chromosomal arm. Lastly, using transposon mutagenesis coupled with deep sequencing (Tn-seq), we identified a ∼500 kb region surrounding the native parS cluster that is tolerable to the insertion of a second parS cluster without severely affecting cell viability. Our results demonstrate that the genomic distribution of parS sites is highly restricted and is crucial for chromosome segregation in Caulobacter.