Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA

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DNA binding proteins are involved in many cellular processes. The ability of these proteins to bind DNA is often modulated, either directly or indirectly. We determined the binding properties of Bacillus subtilis DnaA to genomic DNA at single nucleotide resolution using in vitro DNA affinity purification and deep sequencing. DnaA is the replication initiator and transcription factor and a AAA+ ATPase found in virtually all bacteria. Like other AAA+ proteins, DnaA binds ATP or ADP, and the identity of the nucleotide influences protein activity. We found that most DNA binding regions had a slightly higher affinity for ATP-DnaA than ADP-DnaA, but that a few regions had a strong preference for binding ATP-DnaA. Although some chromosomal regions were bound by DnaA both in vitro and in vivo, we observed many differences. Notably, we found regions that were bound in vivo that were not detectably bound in vitro. Binding to these regions in vivo required the nucleoid associated protein Rok. Our findings highlight the importance of other factors in the cell that modify association of DnaA with specific chromosomal regions. The general approach, to date used with only a couple of proteins, should be readily adaptable to many other DNA binding proteins.

Vyšlo v časopise: Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA. PLoS Genet 11(5): e32767. doi:10.1371/journal.pgen.1005258
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005258

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