Proteins in archaea bend strands of DNA in a way that’s similar in eukaryotes, new research from HHMI Investigator Karolin Luger and colleagues reveals. That similarity hints at the evolutionary origin of the elaborate folding that eukaryotic cells use to cram their genome into a nucleus.
In the cells of palm trees, humans, and some single-celled microorganisms, DNA gets bent the same way.
By studying the 3-D structure of proteins bound to DNA in microbes called archaea, researchers have turned up surprising similarities to DNA packing in more complicated organisms. “If you look at the nitty gritty, it’s identical,” says Howard Hughes Medical Institute Investigator Karolin Luger, a structural biologist and biochemist at the University of Colorado Boulder. “It just blows my mind.”
The archaeal DNA folding, reported August 10 in Science, hints at the evolutionary origins of genome folding, a process that involves bending DNA and one that is remarkably conserved across all eukaryotes (organisms that have a defined nucleus surrounded by a membrane). Like Eukarya and Bacteria, Archaea represents one of the three domains of life. But Archaea is thought to include the closest living relatives to an ancient ancestor that first hit on the idea of folding DNA.
Scientists have long known that cells in all eukaryotes, from fish to trees to people, pack DNA in exactly the same way. DNA strands are wound around a “hockey puck” composed of eight histone proteins, forming what’s called a nucleosome. Nucleosomes are strung together on a strand of DNA, forming a “beads on a string” structure. The universal conservation of this genetic necklace raises the question of its origin.
If all eukaryotes have the same DNA bending style, “then it must have evolved in a common ancestor,” says study coauthor John Reeve, a microbiologist at Ohio State University. “But what that ancestor was, is a question no-one asked.”
Earlier work by Reeve had turned up histone proteins in archaeal cells. But, archaea are prokaryotes (microorganisms without a defined nucleus), so it wasn’t clear just what those histone proteins were doing. By examining the detailed structure of a crystal that contained DNA bound to archaeal histones, the new study reveals exactly how DNA packing works.
Luger and her colleagues wanted to make crystals of the histone-DNA complex in Methanothermus fervidus, a heat-loving archaeal species. Then, they wanted to bombard the crystals with X-rays. This technique, called X-ray crystallography, yields precise information about the position of each and every amino acid and nucleotide in the molecules being studied. But growing the crystals was tricky (the histones would stick to any given stretch of DNA, making it hard to create consistent histone-DNA structures), and making sense of the data they could get was no easy feat. “It was a very gnarly crystallographic problem,” says Luger.
Yet Luger and her colleagues persisted. Postdoctoral researcher Sudipta Bhattacharyya “beat this thing with everything he could,” says Luger, and ultimately solved the structure. The researchers revealed that despite using a single type of histone (and not four as do eukaryotes), the archaea were folding DNA in a very familiar way, creating the same sort of bends as those found in eukaryotic nucleosomes.
But there were differences, too. Instead of individual beads on a string, the archaeal DNA formed a long superhelix, a single, large curve of already twisty DNA strands. “In Archaea, you have one single building block,” Luger says. “There is nothing to stop it. It’s almost like it’s a continuous nucleosome, really.”
This superhelix formation, it turns out, is important. When postdoctoral researcher Francesca Mattiroli, together with the Santangelo lab, created mutations that interfered with this structure, the cells had trouble growing under stressful conditions. What’s more, the cells seemed to not be using a set of their genes properly. It’s clear with these mutations that they can’t form these stretches,” says Mattiroli, of the University of Colorado Boulder.
The results suggest that the archaeal DNA folding is an early prototype of the eukaryotic nucleosome. “I don’t think there’s any doubt that it’s ancestral,” Reeve says.
Still, many questions remain. Luger says she’d like to look for the missing link — a nucleosome-like structure that bridges the gap between the simple archaeal fold and the elaborate nucleosome found in eukaryotes, which can pack a huge amount of DNA into a small space and regulate gene behavior in many ways. “How did we get from here to there?” she asks.
Francesca Mattiroli et al. “Structure of Histone-based Chromatin in Archaea,” Science 357 (2017): 609-12, doi: 10.1126/science.aaj1849