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Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid‐associated protein Rok in Bacillus subtilis
Author(s) -
Seid Charlotte A.,
Smith Janet L.,
Grossman Alan D.
Publication year - 2017
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/mmi.13590
Subject(s) - dnaa , biology , operon , bacillus subtilis , nucleoid , gene , genetics , transcription (linguistics) , dna replication , dna binding protein , promoter , microbiology and biotechnology , origin of replication , transcription factor , mutant , gene expression , escherichia coli , bacteria , linguistics , philosophy
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.