Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid‐associated protein Rok in Bacillus subtilis. Issue 5 (3rd January 2017)

• Record Type: Journal Article
• Authors: Seid, Charlotte A.; Smith, Janet L.; Grossman, Alan D.
• Is Part Of: Molecular microbiology. Volume 103:Issue 5(2017)
• Page Start: 798
• Page End: 817
• Publication Date: 2017-01-03
• Subjects: Molecular microbiology -- Periodicals; 572.829
• DOI: 10.1111/mmi.13590
• Languages: English
• ISSNs: 0950-382X

Abstract

Summary: We identified interactions between the conserved bacterial replication initiator and transcription factor DnaA and the nucleoid‐associated protein Rok of Bacillus subtilis . DnaA binds directly to clusters of DnaA boxes at the origin of replication and elsewhere, including the promoters of several DnaA‐regulated genes. Rok, an analog of H‐NS from gamma‐proteobacteria that affects chromosome architecture and of Lsr2 from Mycobacteria, binds A+T‐rich sequences throughout the genome and represses expression of many genes. Using crosslinking and immunoprecipitation followed by deep sequencing (ChIP‐seq), we found that DnaA was associated with eight previously identified regions containing clusters of DnaA boxes, plus 36 additional regions that were also bound by Rok. Association of DnaA with these additional regions appeared to be indirect as it was dependent on Rok and independent of the DNA‐binding domain of DnaA. Gene expression and mutant analyses support a model in which DnaA and Rok cooperate to repress transcription of yxaJ, the yybNM operon and the sunA‐bdbB operon. Our results indicate that DnaA modulates the activity of Rok. We postulate that this interaction might affect nucleoid architecture. Furthermore, DnaA might interact similarly with Rok analogues in other organisms. Abstract : The bacterial replication initiator and transcription factor DnaA associates with specific chromosomal regions by binding directly to recognition sequences in the DNA. We found that in Bacillus subtilis DnaA is also associated with many chromosomal regions by associating with the nucleotide associated protein Rok (an H‐NS analogue). DnaA stimulates the ability of Rok to bind DNA and together, and these two proteins appear to modulate expression of several genes.