Faster rates of evolution are linked to tiny genomes
Scientists uncover evidence that connects increased rates of mutation to changes in genome size in prokaryotes

Date:
August 6, 2020
Source:
Okinawa Institute of Science and Technology (OIST) Graduate
University
Summary:
Inside every cell lies a genome - a full set of DNA that contains
the instructions for building an organism. Across the biological
world, genomes show a staggering diversity in size but scientists
still don't fully understand why. Now, scientists have found a
link between mutation rate - how quickly the DNA sequence changes
- and genome size. Writing in Current Biology, the researchers
reported that prokaryotes with higher mutation rates lose genes
at a faster pace, and therefore have smaller genomes.



FULL STORY ========================================================================== Inside every cell lies a genome -- a full set of DNA that contains the instructions for building an organism. Across the biological world,
genomes show a staggering diversity in size. For example, the genome
of the Japanese white flower, Paris japonica, is over 150 billion base
pairs, meaning that almost 100 meters of DNA is squeezed into each
cell. In comparison, single- celled prokaryotes, like bacteria, have
tiny genomes, averaging less than 5 million base pairs. Some prokaryotes
have even smaller genomes that are fewer than 500,000 base pairs. But scientists still don't fully understand the driving forces responsible
for reducing the size of genomes.


==========================================================================
Now, in an international collaboration, led by the Okinawa Institute of
Science and Technology Graduate University (OIST) and the University of
Sydney, and including researchers from the University of the Ryukyus,
the Tokyo Institute of Technology, and RIKEN, scientists have found a
link between mutation rate - - how quickly the DNA sequence changes --
and genome size. Writing in Current Biology, the researchers reported
that prokaryotes with higher mutation rates lose genes at a faster pace,
and therefore have smaller genomes.

"This was a really surprising result," said Professor Tom Bourguignon,
co-first author of the study and head of the Evolutionary Genomics Unit
at OIST.

"Currently, the most accepted idea is that population size is the
main factor that determines genome size in prokaryotes, particularly in endosymbionts, but our research challenges this view." Endosymbionts are organisms that live inside the bodies or cells of other organisms,
and typically have much smaller genomes than their free-living
counterparts. The Evolutionary Genomics Unit researches an endosymbiont
called Blattabacterium, a bacterial species that lives inside cockroaches
and termites and provides their hosts with vital nitrogen-containing
nutrients. But only a small number of these bacteria are passed on from a mother insect host to a daughter insect host, which keeps their effective population size very low.

"At small population sizes, natural selection is much less effective,
and evolution is driven more strongly by chance," said Dr. Yukihiro Kinjo, co-first author and a postdoctoral scholar from the Evolutionary Genomics
Unit. "Without enough selection pressure to maintain specific genes,
mutations can arise that inactive and erode these genes, eventually
leading to their total loss from the genome." While population size
as a driving force for genome reduction may be an attractive idea,
many free-living prokaryotes that live in larger populations have also
evolved smaller genomes, suggesting that it's only part of the story.

Additional explanations have also been proposed but, until now, the
mutation rate -- or the speed at which evolution occurs -- has been
overlooked.



==========================================================================
In the study, the scientists collected genome data from a diverse range
of prokaryotes, including strains from two endosymbiotic lineages and
seven free- living lineages.

For each lineage, the team constructed an evolutionary tree that showed
how the strains had diverged from each other. With the help of the
OIST Biological Complexity Unit, led by Professor Simone Pigolotti,
the scientists then created models that reconstructed how gene loss
had occurred in each strain. They then estimated the mutation rate,
population size and selection pressure for each strain and compared it
to the amount of gene loss.

Surprisingly, the scientists did not find a clear link between estimated population size and rate of gene loss. Instead, they found a relationship between mutation rate and gene loss for seven out of the nine lineages
studied, with higher mutation rates associated with faster rates of gene
loss, resulting in smaller genomes.

"Although we haven't established a cause, there is a theoretical
prediction that explains this observation; if the rate of mutation
outweighs a selection pressure to maintain a gene, the gene will be lost
from the genome," said Dr.

Kinjo.

The scientists also found clues as to how the gene loss occurred, as
strains with smaller genomes had lost genes involved in repairing DNA.



==========================================================================
"DNA repair genes fix damaged DNA, so when they are lost the mutation
rate of a strain can quickly increase. Most mutations are harmful,
so this can quickly inactivate other genes and drive their loss from
the genome. If some of these inactivated genes are also involved in
DNA repair, this can further accelerate mutation rate and gene loss,"
explained Professor Gaku Tokuda, from the University of the Ryukyus.

Although the answers to how gene loss occurs are becoming clearer,
whether there are evolutionary reasons behind why prokaryotes increase
their rate of mutation to shrink their genome, and if so, what these
reasons are, remains an open question.

"Figuring out the evolutionary explanation for what we see is really complicated. It could be that an increased rate of mutation occurs
to provide an adaptive advantage, such as the removal of unwanted or unnecessary genes.

But we still can't rule out the possibility that the increased rate of
mutation is non-adaptive and due to chance," said Dr. Kinjo.

Overall, their findings shed new light on the evolution of small genomes, prompting a re-think of the current dominant idea of genome reduction
being driven by small population sizes.

"Unlike with population size, our results suggest that mutation rate
could drive genome reduction in both free-living and endosymbiotic
prokaryotes. This could be the first step in comprehensively understanding
what drives changes in genome size across all prokaryotes," said
Prof. Bourguignon.


========================================================================== Story Source: Materials provided by Okinawa_Institute_of_Science_and_Technology_(OIST)
Graduate_University. Original written by Dani Ellenby. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. Thomas Bourguignon, Yukihiro Kinjo, Paula Villa-Marti'n, Nicholas V.

Coleman, Qian Tang, Daej A. Arab, Zongqing Wang, Gaku Tokuda, Yuichi
Hongoh, Moriya Ohkuma, Simon Y.W. Ho, Simone Pigolotti, Nathan Lo.

Increased Mutation Rate Is Linked to Genome Reduction in
Prokaryotes.

Current Biology, 2020; DOI: 10.1016/j.cub.2020.07.034 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200806111850.htm

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