Multiple cis-Acting rDNAs Contribute to Nucleoid Separation and Recruit the Bacterial Condensin Smc-ScpAB

Abstract

Summary: Condensins load onto DNA to organize chromosomes. Smc-ScpAB clearly loads onto the parS sites bound by Spo0J, but other loading site(s) must operate independently of parS. In this study, we asked where and how Smc-ScpAB normally selects its loading site. Our results suggest that rDNA is also a loading site. A pull-down assay revealed that Smc-ScpAB preferentially loads onto rDNA in the wild-type cell and even in a Δspo0J mutant but not in a Δsmc mutant. Moreover, we showed that deletion mutants of rDNAs cause a defect in nucleoid separation, and at least two rDNAs near oriC are essential for separation. Full-length rDNA, including promoters, is required for loading and nucleoid separation. A synthetic defect by deletions of both rDNA and spo0J resulted in more aberrant nucleoid separation. We propose that a single-stranded segment of DNA that is exposed at highly transcribed rRNA operons would become a target for Smc-ScpAB loading. : Where and how bacterial condensin normally selects its loading site is not known. Yano and Niki show that Smc-ScpAB preferentially loads onto rDNA near the replication origin to compact newly replicated chromosomal DNA. This suggests that two loading pathways for Smc-ScpAB cooperatively function to manifest the physical separation of nucleoids. Keywords: chromosome, bacteria, oriC resolution, transcription, pull-down, Smc, topological binding, single-stranded DNA, R-loop