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DNA replication initiation in Bacillus subtilis: Structural and functional characterization of the essential DnaA-DnaD interaction

Martin, Eleyna; Williams, Huw E.L.; Pitoulias, Matthaios; Stevens, Daniel; Winterhalter, Charles; Craggs, Timothy D.; Murray, Heath; Searle, Mark S.; Soultanas, Panos

Authors

Eleyna Martin

Matthaios Pitoulias

Daniel Stevens

Charles Winterhalter

Timothy D. Craggs

Heath Murray

Mark S. Searle



Abstract

© 2018 The Author(s). The homotetrameric DnaD protein is essential in low G+C content gram positive bacteria and is involved in replication initiation at oriC and re-start of collapsed replication forks. It interacts with the ubiquitously conserved bacterial master replication initiation protein DnaA at the oriC but structural and functional details of this interaction are lacking, thus contributing to our incomplete understanding of the molecular details that underpin replication initiation in bacteria. DnaD comprises N-terminal (DDBH1) and C-terminal (DDBH2) domains, with contradicting bacterial two-hybrid and yeast two-hybrid studies suggesting that either the former or the latter interact with DnaA, respectively. Using Nuclear Magnetic Resonance (NMR) we showed that both DDBH1 and DDBH2 interact with the N-terminal domain I of DnaA and studied the DDBH2 interaction in structural detail. We revealed two families of conformations for the DDBH2-DnaA domain I complex and showed that the DnaA-interaction patch of DnaD is distinct from the DNA-interaction patch, suggesting that DnaD can bind simultaneously DNA and DnaA. Using sensitive single-molecule FRET techniques we revealed that DnaD remodels DnaA-DNA filaments consistent with stretching and/or untwisting. Furthermore, the DNA binding activity of DnaD is redundant for this filament remodelling. This in turn suggests that DnaA and DnaD are working collaboratively in the oriC to locally melt the DNA duplex during replication initiation.

Citation

Soultanas, P., Searle, M. S., Murray, H., Craggs, T. D., Winterhalter, C., Stevens, D., …Martin, E. (2019). DNA replication initiation in Bacillus subtilis: Structural and functional characterization of the essential DnaA-DnaD interaction. Nucleic Acids Research, 47(4), 2101-2112. https://doi.org/10.1093/nar/gky1220

Journal Article Type Article
Acceptance Date Nov 22, 2018
Online Publication Date Dec 8, 2018
Publication Date Feb 28, 2019
Deposit Date Nov 23, 2018
Publicly Available Date Jun 24, 2020
Journal Nucleic Acids Research
Print ISSN 0305-1048
Electronic ISSN 1362-4962
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 47
Issue 4
Pages 2101-2112
DOI https://doi.org/10.1093/nar/gky1220
Keywords Genetics
Public URL https://nottingham-repository.worktribe.com/output/1303012
Publisher URL https://academic.oup.com/nar/article/47/4/2101/5235411

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