Avoiding chromosome pathology when replication forks collide

Abstract

Chromosome duplication normally initiates through the assembly of replication fork complexes at defined origins1,2. DNA synthesis by any one fork is thought to cease when it meets another travelling in the opposite direction, at which stage the replication machinery may simply dissociate before the nascent strands are finally ligated. But what actually happens is not clear. Here we present evidence consistent with the idea that every fork collision has the potential to threaten genomic integrity. In Escherichia coli this threat is kept at bay by RecG DNA translocase3 and by single-strand DNA exonucleases. Without RecG, replication initiates where forks meet through a replisome assembly mechanism normally associated with fork repair, replication restart and recombination4,5, establishing new forks with the potential to sustain cell growth and division without an active origin. This potential is realized when roadblocks to fork progression are reduced or eliminated. It relies on the chromosome being circular, reinforcing the idea that replication initiation is triggered repeatedly by fork collision. The results reported raise the question of whether replication fork collisions have pathogenic potential for organisms that exploit several origins to replicate each chromosome.

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Figure 1: PriA triggers DnaA-independent chromosome replication in the absence of RecG.
Figure 2: Replisome collision triggers DnaA-independent replication.
Figure 3: Effect of RecBCD activity and oriC duplication on DnaA-independent replication.
Figure 4: Effect of recG, tus and growth phase on chromosome marker frequencies.

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Accessions

Gene Expression Omnibus

Data deposits

Deep sequencing data have been deposited with NCBI Gene Expression Omnibus under accession number GSE41975.

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Acknowledgements

We thank T. Horiuchi and D. Sherratt for E. coli strains, A. Mahdi for help with DNA extractions, S. Malla and M. Blythe for deep sequencing, S. Demolli and D. Ivanova for control experiments, and C. Buckman and L. Harris for assistance. This work was supported by grants from the MRC (R.G.L., G0800970), the Leverhulme Trust (C.J.R.) and the BBSRC (C.A.N., BB/E023754/1).

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C.J.R. and R.G.L. initiated and directed the project. C.J.R., A.L.U., A.S., C.A.N. and R.G.L. performed the experimental work. C.J.R., A.L.U., C.A.N. and R.G.L. analysed the data and wrote the paper.

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Correspondence to Christian J. Rudolph.

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The authors declare no competing financial interests.

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Rudolph, C., Upton, A., Stockum, A. et al. Avoiding chromosome pathology when replication forks collide. Nature 500, 608–611 (2013). https://doi.org/10.1038/nature12312

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