Scientists have discovered a form of natural selection that does not depend on DNA.
Evolution and natural selection take place at the DNA level, as genes mutate and genetic traits either remain or are lost over time. But now scientists believe that evolution can occur on a completely different scale – not transmitted through genes, but through molecules stuck to their surface.
These molecules, known as methyl groups, change the structure of DNA and can turn genes on and off. The changes are known as 'epigenetic modifications', meaning they appear 'above' or 'above' the genome. In many organisms, DNA is dotted with methyl groups, but creatures like fruit flies and roundworms have lost the genes they need.
Another organism, the yeast Cryptococcus neoformans, also lost key genes for methylation sometime in the Cretaceous, about 50-150 million years ago. But it is noteworthy that in its current form, the fungus still has methyl groups in its genome. Now, according to a theoretical study published January 16 in the journal Cell, scientists have been able to hypothesize that C. neoformans managed to maintain epigenetic changes for tens of millions of years thanks to a new way of evolution.
“We didn't expect the secret of evolution to be revealed,” says senior author Dr. Hiten Madhani, professor of biochemistry and biophysics at the University of California, San Francisco.
Scientists are studying C. neoformans to better understand how yeast causes fungal meningitis in humans. According to the UCSF, the fungus infects people with weak immune systems and is responsible for about 20% of all HIV / AIDS deaths. Madhani and his colleagues spend their days digging through the genetic code of C. neoformans, looking for the critical genes that help yeast enter human cells. But the team was surprised when reports surfaced that the genetic material was decorated with methyl groups.
'When we found out that [C. neoformans] DNA methylation … I thought we should look at this without even knowing what we would find, ”Madhani said.
In vertebrates and plants, cells add methyl groups to DNA using two enzymes. The first, called 'de novo methyltransferase', attaches methyl groups to unstained genes. The enzyme stains each half of the helical DNA strand with the same methyl group pattern, creating a symmetrical design. During cell division, the double helix unfolds and builds two new DNA strands from the corresponding halves. At this point, an enzyme called a 'maintenance methyltransferase' starts copying all methyl groups from the original chain to the newly built half.
Madhani and his colleagues studied existing evolutionary trees to trace the history of C. neoformans over time, and found that the ancestor of yeast had both enzymes necessary for DNA methylation during the Cretaceous Period. But somewhere, C. neoformans lost the gene needed to make de novo methyltransferase. Without the enzyme, the body could no longer add new methyl groups to its DNA – it could only copy existing methyl groups.
In theory, even working alone, a maintenance enzyme could retain DNA in methyl groups indefinitely – if it could make a perfect copy every time.
In fact, the enzyme makes mistakes and loses methyl groups every time a cell divides, the team found. When grown in a Petri dish, C. neoformans cells sometimes accidentally acquire new methyl groups, similar to how random mutations occur in DNA. However, cells lost methyl groups about 20 times faster than they could get new ones.
The team estimates that within about 7,500 generations, every last methyl group will disappear, leaving nothing left for the enzyme to copy. Given the rate at which C. neoformans multiplies, the yeast should have lost all of its methyl groups within about 130 years. Instead, he retained the epigenetic edits for tens of millions of years.
Many mysteries still surround DNA methylation in C. neoformans. In addition to copying methyl groups between DNA strands, the maintenance methyltransferase appears to be important when it comes to how yeast causes infections in humans, according to Madhani's 2008 study. Without a whole enzyme, the body cannot penetrate cells as efficiently.
“We have no idea why this is necessary for effective infection,” Madhani said.
The enzyme also requires a lot of chemical energy to function and copies only methyl groups to the clean half of the replicated DNA strands. In comparison, the equivalent enzyme in other organisms does not require additional energy to function and sometimes interacts with naked DNA devoid of any methyl groups, according to a report published on the bioRxiv preprint server.
Further research will show how methylation works in C. neoformans and whether this new form of evolution appears in other organisms.
