Abstract
Regulating DNA replication is essential for all living cells. The DNA replication initiation factor DnaA is highly conserved in prokaryotes and is required for accurate initiation of chromosomal replication at oriC. DnaA-independent free-living bacteria have not been identified. The dnaA gene is absent in plastids and some symbiotic bacteria, although it is not known when or how DnaA-independent mechanisms were acquired. Here, we show that the degree of dependency of DNA replication on DnaA varies among cyanobacterial species. Deletion of the dnaA gene in Synechococcus elongatus PCC 7942 shifted DNA replication from oriC to a different site as a result of the integration of an episomal plasmid. Moreover, viability during the stationary phase was higher in dnaA disruptants than in wild-type cells. Deletion of dnaA did not affect DNA replication or cell growth in Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, indicating that functional dependency on DnaA was already lost in some nonsymbiotic cyanobacterial lineages during diversification. Therefore, we proposed that cyanobacteria acquired DnaA-independent replication mechanisms before symbiosis and such an ancestral cyanobacterium was the sole primary endosymbiont to form a plastid precursor.
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Acknowledgements
We thank Drs Kazuharu Arakawa and Motohiro Akashi for advice on bioinformatics analyses; Dr Yuh Shiwa for advice on the analysis of next-generation sequencing data; and Tomoko Kojima for comments on the manuscript. This study was funded by the Sasagawa Scientific Research Grant from the Japan Science Society (to RO), by the MEXT-supported Program for Strategic Research Foundation at Private Universities, 2013–2017 (S1311017), by Grant-in-Aid for Scientific Research (C) to YK (15K07368), and by Grants-in-Aid for Young Scientists (B) to SW (25850056).
Author contributions
RO, SW and HY designed the experiments. RO performed the experiments. SE constructed Anabaena mutant strains. RO and YK analyzed Repli-seq and RNA sequencing data. RO, SW, YK, SE, TC and HY wrote the paper.
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Ohbayashi, R., Watanabe, S., Ehira, S. et al. Diversification of DnaA dependency for DNA replication in cyanobacterial evolution. ISME J 10, 1113–1121 (2016). https://doi.org/10.1038/ismej.2015.194
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DOI: https://doi.org/10.1038/ismej.2015.194
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