The DNA replication initiation protein DnaD recognises a specific strand of the Bacillus subtilis chromosome origin

Winterhalter, Charles; Pelliciari, Simone; Stevens, Daniel; Fenyk, Stepan; Marchand, Elie; Cronin, Nora B; Soultanas, Panos; Costa, Tiago R.D.; Costa, Tiago R D; Ilangovan, Aravindan; Murray, Heath

Abstract

Genome replication is a fundamental biological activity shared by all organisms. Chromosomal replication proceeds bidirectionally from origins, requiring the loading of two helicases, one for each replisome. However, the molecular mechanisms underpinning helicase loading at bacterial chromosome origins (oriC) are unclear. Here we investigated the essential DNA replication initiation protein DnaD in the model organism Bacillus subtilis. A set of DnaD residues required for ssDNA binding was identified, and photo-crosslinking revealed that this ssDNA binding region interacts preferentially with one strand of oriC. Biochemical and genetic data support the model that DnaD recognizes a new single-stranded DNA (ssDNA) motif located in oriC, the DnaD Recognition Element (DRE). Considered with single particle cryo-electron microscopy (cryo-EM) imaging of DnaD, we propose that the location of the DRE within oriC orchestrates strand-specific recruitment of helicase during DNA replication initiation. These findings significantly advance our mechanistic understanding of bidirectional replication from a bacterial chromosome origin.

Citation

Winterhalter, C., Pelliciari, S., Stevens, D., Fenyk, S., Marchand, E., Cronin, N., Costa, T. R., Soultanas, P., Costa, T. D., Ilangovan, A., & Murray, H. (2023). The DNA replication initiation protein DnaD recognises a specific strand of the Bacillus subtilis chromosome origin. Nucleic Acids Research, 51(9), 4322-4340. https://doi.org/10.1093/nar/gkad277

• Journal Article Type: Article
• Acceptance Date: Apr 4, 2023
• Online Publication Date: Apr 24, 2023
• Publication Date: May 22, 2023
• Deposit Date: May 5, 2023
• Publicly Available Date: May 11, 2023
• Journal: Nucleic Acids Research
• Print ISSN: 0305-1048
• Electronic ISSN: 1362-4962
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 51
• Issue: 9
• Pages: 4322-4340
• DOI: https://doi.org/10.1093/nar/gkad277
• Keywords: Genome integrity, repair and replication
• Public URL: https://nottingham-repository.worktribe.com/output/20008612
• Publisher URL: https://academic.oup.com/nar/article/51/9/4322/7137456?login=false