eLife: Captured the unstable rate at which DNA replicates proteins in bacteria

Cell division is the foundation of life, which allows organisms to grow, repair and multiply
.
For a cell to divide, all DNA (genome) within the cell must first be copied, a process known as DNA replication
.
But for scientists, the precise dynamics of the protein mechanisms that replicate DNA—complexes—have been difficult to determine
.

Now, researchers at the Okinawa Institute of Science and Technology (OIST) in Japan have developed a new model that can determine the rate of change in the genome of
complex replicating bacteria.
The model combined experiments showed that some parts of DNA replicated faster than others and revealed an interesting link
between replication speed and error rate.
The study was published in the journal eLife on July 25, 2022
.

"The machines that replicate DNA are amazing — they're very fast, they're very precise," said
Simone Pigolotti, an associate professor at OIST and head of the Department of Biological Complexity.
"Understanding these machines can tell us what is important to the cell – what mistakes are tolerable, what errors are intolerable, and how fast
replication should be.
"

The model relies on measuring the richness
of different DNA locations in a constantly dividing bacterial cell population.
In bacteria, to begin DNA replication, two complexes are attached to the DNA at a fixed starting point and move in opposite directions along the DNA loop, replicating the DNA until they meet
at the other end.
This means that the DNA closest to the starting point is copied first, and the DNA closest to the end point is copied
last.

"If you let a group of bacteria grow freely, then at any given point in time, most cells will be in the process of
cell division.
Because DNA replication always starts at the same location, this means that if you sequence all the DNA, the abundance of DNA near the starting point will be higher, and the abundance of DNA near the end point will be much lower,"
explains Professor Piglotti.

In this study, by analyzing the characteristics of the distribution curve, the researchers were able to determine the exact velocity
of the protein machine.
They found that as the temperature increased, the replication rate also accelerated
.
More interestingly, the researchers found that the rate of the complex also differed at different locations in
the genome.

Professor Piglotti speculates that one potential cause of fluctuations in replication rates may be the limited resources required for replication, such as nucleotides, which are components of DNA
.

In the United States, when conditions are good, individual bacterial cells divide every 25 minutes
.
But the process of replicating DNA takes longer — about 40 minutes
.
Thus, in order to maintain a high growth rate, multiple copies of the genome are replicated simultaneously, which increases the number of
complexes at work.
Competition for nucleotides can then cause the complex to slow down
.

More evidence supports this hypothesis
.
In cryogenic and malnourished media, fluctuations in replication speed disappear when bacteria grow at a low rate, replicating only one genome at a time
.

Interestingly, the researchers also found that oscillations in replication velocity also matched
oscillations in mutation rates recorded in other studies.
When they stacked the two patterns together, they found that regions of the genome that replicate faster also have higher mutation rates
.

Professor Piglotti said: "It seems intuitive – if we think of an action, like typing on a keyboard, the faster we type, the more
likely we are to make mistakes.
" "So we think that when the complex goes faster, they have a higher
error rate.
"

Professor Pigolotti's next step is to determine how the rate of replication in mutant strains changes E.
coli such as those cells
that lack proteins to help replicate.
He was also curious to see if this pattern would also apply to other strains of bacteria
.

"This is a very exciting research direction," Professor Piglotti said
.
"All the work was done in collaboration with others here
.
This kind of interdisciplinary collaboration can only happen at OIST
.
”