Ancient Microbes Folded their DNA Similarly to Modern Life Forms

As life evolved on Earth, from simple one-celled microbes to complex plants, animals and humans, their DNA grew. And that created a problem: how do you pack more and more DNA into roughly the same-sized cellular compartment? Life's solution: fold it up into a ball. Reporting in the August 10 edition of the journal Science, researchers have discovered that microbes called archaea started folding their DNA in a way very similar to that of modern plants and animals, long before complex life evolved.

"It was our great astonishment," says Sudipta Bhattacharyya, a postdoctoral researcher in molecular biosciences at The University of Texas at Austin and one of two first authors of the new paper.

Scientists have long known that cells in all eukaryotes (organisms that have a defined nucleus surrounded by a membrane), 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 stretch of double stranded 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—one of three domains of life, along with eukaryotes and bacteria—have no defined nucleus, so it wasn't clear just what those histone proteins were doing. By examining the detailed 3D structure of the archaeal histones bound to DNA in a crystal, the new study reveals exactly how DNA packing works. It also sheds light on the ancestral question: the closest living relatives to the ancient ancestor that first hit on the idea of folding DNA are archaea.

Before this discovery could be made, Howard Hughes Medical Institute Investigator Karolin Luger, a structural biologist and biochemist at the University of Colorado Boulder, and her colleagues had to make crystals of the histone-DNA complex in Methanothermus fervidus, a heat-loving archaeal species. Then, they had to bombard the crystals with X-rays. This technique, called X-ray crystallography, yields precise information about the position of each 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. She says UT Austin's Bhattacharyya, who currently works in the Department of Molecular Biosciences and in the lab of professor Rasika Harshey, "beat this thing with everything he could," and ultimately solved the structure. The researchers revealed that despite using a single type of histone (and not four as eukaryotes do), 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 histone-DNA complex formed a long helical structure where a double-stranded DNA molecule is "supertwisted" as it wraps around a continuous histone column. The results suggest that the archaeal DNA folding is an early prototype of the eukaryotic nucleosome.

In any living organism, the size of its genetic material is so large that without folding, it would extend approximately 400 times (for bacteria like E. coli) to 15,000 times (for human cells) farther than the width of the cell. But cells can't grow that much larger—they would no longer be able to absorb enough nutrients, among other things. Therefore, every organism has its own way to package the DNA inside its cell volume.

Support for this research was provided by the U.S. National Institutes of Health, the European Molecular Biology Organization, the Dutch Cancer Society and the Howard Hughes Medical Institute.