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DNA replication is tightly controlled to ensure accurate inheritance of genetic information. In all organisms, initiator proteins possessing AAA+ (ATPases associated with various cellular activities) domains bind replication origins to license new rounds of DNA synthesis (1). In bacteria the master initiator protein, DnaA, is highly conserved and has two crucial DNA binding activities (2). DnaA monomers recognize the replication origin (oriC) by binding double-stranded DNA sequences (DnaA-boxes); subsequently, DnaA filaments assemble and promote duplex unwinding by engaging and stretching a single DNA strand (3-5). While the specificity for duplex DnaA-boxes by DnaA has been appreciated for over 30 years, the sequence specificity for single-strand DNA binding has remained unknown. Here we identify a new indispensable bacterial replication origin element composed of a repeating trinucleotide motif that we term the DnaA-trio. We show that the function of the DnaA-trio is to stabilize DnaA filaments on a single DNA strand, thus providing essential precision to this binding mechanism. Bioinformatic analysis detects DnaA-trios in replication origins throughout the bacterial kingdom, indicating that this element is part of the core oriC structure. The discovery and characterization of the novel DnaA-trio extends our fundamental understanding of bacterial DNA replication initiation, and because of the conserved structure of AAA+ initiator proteins these findings raise the possibility of specific recognition motifs within replication origins of higher organisms., |\ The master bacterial DNA replication initiator, DnaA, is a highly conserved multifunctional protein that utilizes distinct domains to achieve its two key DNA binding activities. DnaA recognizes double-stranded (ds)DNA [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2008.07.044 Byline: Heath Murray (1), Jeff Errington (1) Keywords: CELLBIO; CELLCYCLE; MICROBIO Abstract: Regulation of DNA replication and segregation is essential for all cells. Orthologs of the plasmid partitioning genes parA, parB, and parS are present in bacterial genomes throughout the prokaryotic evolutionary tree and are required for accurate chromosome segregation. However, the mechanism(s) by which parABS genes ensure proper DNA segregation have remained unclear. Here we report that the ParA ortholog in B. subtilis (Soj) controls the activity of the DNA replication initiator protein DnaA. Subcellular localization of several Soj mutants indicates that Soj acts as a spatially regulated molecular switch, capable of either inhibiting or activating DnaA. We show that the classical effect of Soj inhibiting sporulation is an indirect consequence of its action on DnaA through activation of the Sda DNA replication checkpoint. These results suggest that the pleiotropy manifested by chromosomal parABS mutations could be the indirect effects of a primary activity regulating DNA replication initiation. Author Affiliation: (1) Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK Article History: Received 3 March 2008; Revised 25 May 2008; Accepted 31 July 2008 Article Note: (miscellaneous) Published: October 2, 2008

Author(s): Tomas T. Richardson; Omar Harran; Heath Murray Nature 534, 412416 (2016); doi:10.1038/nature17962 In Fig. 2c of this Letter, the rectangle at the bottom right corner was erroneously labelled ADP [...]