In nature, biological arms races are common. Cheetahs, for example, have evolved a streamlined body shape that allows them to sprint quickly, allowing them to feast on similarly swift gazelles, the quickest of which may be able to avoid predation. Immune cells create proteins to combat pathogens, which may acquire mutations to elude detection at the molecular level.
Other games of one-upmanship take place within the genome, though they are less well-known. Biologists at the University of Pennsylvania have discovered evidence of a two-sided genomic arms race involving repeated DNA segments known as satellites in a new study. In the arms race, fast-developing proteins that bind those satellites are "opposing" the swiftly evolving satellites.
Satellite DNA does not encode genes, but it can help with important biological processes like the development of molecular machines that process and maintain chromosomes. When satellite repeats are not appropriately managed, these critical processes can be harmed. Cancer and infertility are both characterised by such disturbances.
Researchers used two closely related species of fruit flies to investigate this arms race by deliberately generating a species mismatch, pitting one species' satellite DNA against the other's satellite-binding protein, for example. As a result, severe fertility problems developed, highlighting evolution's fragile balance, even at the level of a single chromosome.
"We usually conceive of our genome as a cohesive community of elements that generate or regulate proteins to build a productive and viable individual," says Mia Levine, an assistant professor of biology at Penn and the study's senior author. "This conjures up images of our genomic elements working together, which is largely correct.
"However, we believe that some of these substances are truly harmful to us," she continues. "This unsettling notion implies that there must be a system in place to keep them in control."
The findings, which are likely to apply to humans as well, suggest that when satellite DNA escapes the control of satellite-binding proteins, significant fitness costs can be incurred, including effects on molecular pathways important for fertility and possibly even those involved in cancer development.
"These findings suggest antagonistic evolution between these elements, which could have an impact on these seemingly conserved and critical biochemical pathways," says Cara Brand, a postdoc in Levine's lab and the paper's first author. "It means that to maintain the status quo during evolutionary time, ongoing innovation is essential."
Evolutionary conundrum
It has long been known that the genome is made up of more than just genes. Long tracts of "gobbledygook" can be found between genes that produce proteins, according to Levine.
"If genes were words, and the tale of our genome were told in words, these other sections would be incomprehensible," she says. "It was dismissed as genetic nonsense for a long time."
This so-called "junk" includes satellite DNA. Satellite repeats make up nearly half of the genome of the fruit fly Drosophila melanogaster, which is frequently employed as a scientific model organism. Scientists used to believe satellite repeats were unlikely to be doing anything useful in the body because they evolved so quickly without any apparent functional consequence.
Recent research has cast doubt on the "junk DNA" theory, indicating that the "gobbledygook," including satellite repeats, has a number of functions, many of which are connected to preserving genomic integrity and organisation in the nucleus.
"This creates a dilemma," Levine explains. "If these highly repeated areas of the genome perform critical functions or, if not controlled properly, might be harmful, it suggests that we need to keep them under check."
In 2001, a group of scientists proposed a proposal that satellites and satellite binding proteins were coevolving, with satellites quickly evolving and satellite binding proteins evolving to keep up. Scientists have backed up the notion in the two decades after it was first proposed. These experiments used genetic manipulation to introduce a satellite-binding protein from one species into the genome of a closely similar species and investigate what occurs when the two species' genomes clash.
"These gene swaps frequently cause malfunction," Brand explains, "especially disturbing a process that is normally mediated by repetitive DNA-rich sections of the genome."
New evidence-gathering tools
The coevolution theory was supported by these studies. However, it will be unable to confirm that the disruption observed was caused by an interaction between the satellite-binding protein and the satellite DNA until researchers can change both elements experimentally.
Levine and Brand have found a method to achieve just that in their current work. Drosophila simulans, a fruit fly species closely related to Drosophila melanogaster, lacks a satellite repeat that spans 11 million nucleotide base pairs. This satellite was discovered to share a cellular site with a protein known as Maternal Haploid (MH). The researchers also had access to a D. melanogaster mutant strain that didn't have the 11 million base pair repeat.
"It turns out that the fly can live and reproduce without this repeat," Levine explains. "As a result, it provided us with a once-in-a-lifetime opportunity to manipulate both sides of the weapons race."
The researchers employed the CRISPR/Cas9 gene editing method to delete the original MH gene from D. melanogaster and replace it with the D. simulans version of the gene to examine the satellite-binding protein side first. Female flies carrying the D. simulans MH gene had much lower fertility and produced significantly fewer eggs than control females.
Flies that were completely devoid of MH, on the other hand, were unable to reproduce; the embryos were not viable.
"This was fascinating since it demonstrated that satellite-binding proteins are critical, despite their fast evolution," explains Brand. "The gene switch demonstrated that we could resurrect the ability to create embryos. However, another function involving the ovary and egg production was disrupted."
When Brand and Levine examined the ovaries closely, they determined that DNA damage was the apparent reason of diminished egg production and atrophied ovaries. When a cell is damaged, a checkpoint protein is activated, and developmental pathways are halted. Egg production levels were recovered to a higher level when the researchers performed the experiments in a fly with a malfunctioning checkpoint protein.
After that, Levine and Brand were ready to test the other side of the coevolutionary arms race, looking for evidence that the issues with the swapped MH protein were caused by an incompatibility with the 11 million base pair satellite, or if they were operating on an other genetic material. They used a D. melanogaster strain that was missing the repeat in this experiment and discovered that the gene exchange had no effect on these flies. The amounts of DNA damage, egg production, and ovary size were all within normal limits.
The scientists were able to deduce the mechanism behind these findings by looking at the closest human relative of the MH protein, Spartan. Spartan is thought to digest proteins that can become caught on DNA, obstructing various processes and packaging that DNA must go through. "We thought, after all we'd uncovered so far, maybe this erroneous species form of the protein is chewing up something it shouldn't," Levine adds.
Spartan frequently targets Topoisomerase II, or Top2, an enzyme that aids in the resolution of tangles in tightly wrapped and entangled DNA. They overexpressed Top2 to investigate if the deleterious effects of the MH gene mismatch were due to improper degradation of Top2, and discovered that fertility was restored. Top2 reduction, on the other hand, worsened the fertility decline.
"This MH-involved healing process occurs in yeast, flies, and humans across the tree of life," adds Brand. "Nonetheless, these proteins are undergoing rapid or adaptive evolution. This shows that evolutionary innovation is required for this seemingly preserved and crucial process." To put it another way, coevolution must continue apace just to keep this vital channel open.
Beyond flies, there are ramifications
In the future, Brand and Levine will investigate if regions of the genome other than satellites are implicated, as well as other animals, such as mammals, to learn more about the molecular participants in these evolutionary arms races.
"There's no reason to suppose these arms competitions are limited to flies," adds Levine. "The same types of proteins and satellites evolve rapidly in primates, indicating that what we're studying is broadly applicable."
The focus genes in this study play critical functions in human health. Spartan mutations have been linked to cancer, and inadequate satellite DNA management may provide insight into infertility and miscarriage.
"The frequency of miscarriages is staggering, and satellite DNA is unquestionably a source of aneuploidy and genomic instability," says Levine.
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