Cell division is fundamental for life, allowing organisms to grow, repair tissues, and reproduce. For a cell to divide, all the DNA inside the cell (the genome) must first be copied, in a process called DNA replication. But the precise dynamics of replisomes — the protein machinery that copies DNA — has been difficult for scientists to determine.
Now, researchers at the Okinawa Institute of Science and Technology (OIST) in Japan have developed a new model that can determine variations in the speed at which replisomes copy bacterial genomes. The model, combined with experiments, shows that certain sections of DNA are copied faster than others and reveals an intriguing link between replication speed and error rate. The research was published in eLife on July 25, 2022.
“The machines that copy DNA are amazing — they are very fast and very precise,” said Simone Pigolotti, an Associate Professor at OIST who heads the Biological Complexity Unit. “Understanding these machines can tell us what is important for cells — what mistakes are tolerable, what mistakes are not, how fast replication should be.”
The model relies on measuring how abundant different DNA locations are within a population of bacterial cells that are constantly dividing. In bacteria, to start DNA replication, two replisomes attach to the DNA at a set origin point and head in opposite directions along the loop of DNA, copying DNA until they meet on the other side. This means that the DNA closest to the origin point is copied first, while DNA closest to the termination point is copied last.
“If you let a population of bacteria freely grow, then at any given point in time, most cells will be in the process of cell division. Because DNA replication always starts from the same location, this means that if you then sequence all the DNA, there will be a higher abundance of DNA that is closest to the origin point, and a much lower amount of DNA that is closer to the end point,” explained Prof. Pigolotti.
In the study, researchers from the Nucleic Acid Chemistry and Engineering Unit at OIST cultured Escherichia coli (E. coli) bacteria at different temperatures. The Sequencing Section then sequenced the bacteria’s DNA.
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