Life Without DNA Replication Origins

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All cells contain a complete copy of the organism's DNA, packaged into chromosomes. Before cells can divide, their chromosomes must be duplicated. This process is called DNA replication and begins at specific locations on the chromosome called replication origins. Bacteria have a single replication origin but organisms with large chromosomes, such as humans, need many origins. We have found that origins are unnecessary, and that cells without them can grow faster than normal (Hawkins et al. 2013 Nature 503, 544-7).Our research on DNA replication was carried out in Haloferax volcanii, a member of the archaea. The tree of life is split into three groups: eukaryotes, bacteria and archaea. Archaea are microbes renowned for living in extreme conditions such as acid pools and salt lakes. Haloferax volcanii comes from the Dead Sea, we chose it because the enzymes that carry out DNA replication in archaea are similar to those used in eukaryotes.Haloferax volcanii uses several origins to replicate its chromosome. But when all of these origins are removed, the cells actually grow faster. Doing these experiments in humans would be impossible. When origins are eliminated from eukaryotes or bacteria, it prevents DNA replication and leads to death. So how is Haloferax volcanii able to survive?Cells without origins use an alternative method called recombination to start DNA replication. Recombination is a form of DNA repair, it is used to mend breaks in the chromosome. We found that recombination starts DNA replication at random locations on the chromosome, instead of being restricted to a limited number of origins, and this makes the process faster. But this poses a puzzle: if the alternative process using recombination is more efficient, why have replication origins at all?We propose that origins in Haloferax volcanii are selfish genes. Selfish origins need not offer any advantage to the host cell, but they increase their own frequency because they have hijacked the DNA replication machinery. Over the course of evolution, host cells have found a way to regulate origins and this has allowed them to coordinate the timing of DNA replication with cell division. In complex organisms such as humans, origins have become integrated with cellular processes and it is impossible to delete them without detrimental effects.The unusual mode of DNA replication we have discovered in Haloferax volcanii has parallels with cancer. Haloferax volcanii has many copies of its chromosome, this is called polyploidy and helps it to survive when replication and cell division are no longer coordinated. Many cancer cells have mutations in the genes that control DNA replication, and polyploidy is a common feature of cancer. Another consequence of uncoordinated replication is that cancer cells grow faster than ordinary cells. Such accelerated growth is reminiscent of origin-less Haloferax volcanii, which use an alternative mode of replication to outpace other cells.Our work on a microbe from the Dead Sea has shown how surprising results can come from testing long-held assumptions in unusual organisms. But it has given us as many questions as answers:- How does this alternative mechanism of DNA replication work? Does it have negative consequences for the cell?- Does Haloferax volcanii use it all the time? If not, how is it kept in check by 'normal' replication?- Above all, why does Haloferax volcanii grow faster without origins, when other cells would die? We believe that two aspects of this organism are key: recombination and polyploidy.We will use a combination of genetic and biochemical tools that we have developed, to examine the effects of recombination and polyploidy on replication. This work has implications for DNA replication in all organisms - it may contribute to our understanding of how cancer cells evade the checks on replication, and give an insight into how DNA was replicated before the evolution of 'selfish' origins.