Evolution and natural selection occur at the DNA level, as genetic mutations and genetic characteristics either remain or disappear over time. But now, scientists believe evolution may also occur on a completely different scale, not through genes, but through molecules attached to the surface of genes.
Scientists have discovered a natural way to choose from dna that doesn’t depend on
These molecules, called methyl, alter the structure of DNA and turn genes on and off. This change, known as epigenetic modification, means they appear “above” the genome. Methyl is dotted with the DNA of many organisms, including humans, but organisms such as fruit flies and ticks have lost their genes in the evolution process.
Another organism, Cryptococcus neoformans, a common yeast, also lost key genes for methylation during the Cretaceous period, about 50 million to 150 million years ago. But it is worth noting that, in its current form, the fungus’s genome still has methyl. According to a study published January 16 in the journal Cell, scientists now have a theory that a newly discovered evolutionary pattern allows the new cryptococcal to retain epigenetic editing records for tens of millions of years.
Dr. Hiten Madhani, a professor of biochemistry and biophysics at the University of California, San Francisco and lead researcher at the Chan Zuckerberg Biohub, said the scientists behind the study did not expect to find such a well-kept evolutionary secret.
The team studied the new cryptococcal bacteria mainly to better understand how the yeast causes fungal meningitis in humans. The fungus often infects people with a weak immune system, causing about 20 percent of AIDS-related deaths, according to a statement from the University of California, San Francisco. Madhani and his colleagues spent a lot of time excavating the genetic code of the new cryptococcal bacteria, looking for key genes that helped the yeast invade human cells. However, the team was surprised when it was reported that the fungus’s genetic material could be methylmodified.
“When we knew that the new cryptococcal bacteria had DNA methylation … we were not going to be able to do that,” Madhani said. I think we have to understand that we have no idea what we’re going to find. “
In vertebrates and plants, cells can add methyl to DNA with the help of two enzymes. The first enzyme is “dna methylation enzyme” (denovo methyltransferase), which attaches methyl to unmodified genes. The enzyme adds the same pattern of methyl to each spiral DNA chain, forming a symmetrical design. During cell division, the double helix expands and two new DNA strands are constructed from a matching double chain. At this point, the “maintenance transfer methylation prosase” pops up and copies all methyl from the original DNA strandtos to the newly formed DNA strands.
Madhani and his colleagues traced the history of the new cryptococcal bacteria by looking at existing evolutionary trees and found that during the Cretaceous period, the yeast’s ancestors had both enzymes needed for DNA methylation. However, at some point in evolutionary history, the new cryptococcal bacteria lost the genes needed to make DNA from the head methylase. Without this enzyme, organisms can no longer add new methyls to DNA, but can only replicate existing methylsy with DNA methylation maintenance enzymes.
In theory, even working alone, this maintenance enzyme can make DNA methylation exist indefinitely – if a perfect copy is produced each time.
In fact, the team found, the enzyme went wrong every time cells split and lost traces of methyl. When cultured in a covered petri dish, new cryptococcal cells occasionally randomly acquire new methyl, similar to random mutations in DNA. However, cells lose methyl 20 times faster than they get new methyl.
The team estimates that all methylwill will disappear over about 7,500 generations, making it impossible for the enzyme to replicate. Given the rate at which the new cryptococcal bacteria reproduce, the yeast loses all its methylsy in about 130 years. The reality, however, is that the new cryptococcal bacteria retain tens of millions of years of epigenetic editing.
“Because the loss rate of methylation is higher than the yield rate, if there is no mechanism to sustain methylation, the methylation system will slowly disappear over time,” Madhani said. He points out that this mechanism is in fact a natural choice. In other words, while the new cryptococcal bacteria acquire new methyls much more slowly than they lose, methylation greatly improves the “adaptability” of organisms, which means they can compete against less methylated individuals. “Adapted” individuals are more dominant than those with less methyl, so the level of methylation of new cryptococcal bacteria has remained high for millions of years. But what evolutionary advantages can these methyls bring to new species? Madhani says methyl may protect the yeast genome from potentially fatal damage.
The transposon, also known as the “jumpgene,” is a class of DNA that jumps around the genome at will. They also often insert themselves in very “inconvenient” positions. For example, a transposon can jump into the middle of a gene necessary for a cell’s survival, causing the cell to lose or die. Fortunately, methyl can hold the rotor and secure it. Madhani says the new cryptococcal bacteria may have maintained a certain level of DNA methylation, possibly to control the transposon.
“No single (methylation) site is particularly important, but on the evolutionary time scale, the overall methylation density is selected for transposons,” Madhani added. “
The DNA methylation of the new cryptococcal bacteria still lingers in many unsolved mysteries. According to a study published by Madhani in 2008, DNA methylation acnosins, in addition to replicating methyl between DNA strands, may also affect the infection of new cryptococcal bacteria in humans. Without a complete maintenance enzyme, the fungus cannot effectively invade human cells. “We don’t know why we need this enzyme to be effective,” Madhani said. “
DNA methylation maintenance enzymes also require a lot of chemical energy to function, and only methyl can be copied to a blank part of the replicated DNA chain. By contrast, the enzyme in other organisms does not require additional energy to function, and sometimes interacts with DNA without any methyl, according to a report published on the preprinted website bioRxiv. Further research will reveal how methylation works in new cryptococcal cells and whether this newly discovered form of evolution will appear in other organisms.