Archaea DNA forms into floppy 'slinkies'

Archaea are one of three domains of life, along with bacteria and the more complex eukaryotes. Now, new research has confirmed that archaea microbes package their DNA like a slinky, which may be the precursor for the more elaborate DNA system of eukaryotes. This way of packaging DNA is unique from that of eukaryotes.

Instead of winding 147 base pairs (bp) around a histone to create "beads on a string," archaea chromatin is a continuous winding of 60-500 bp that can flop open to be 90 degrees out of plane with each other.

Scientists speculate that archaea chromatin may be the precursor for the DNA packaging system of eukaryotes. However, the uniqueness of archaea chromatin packaging doesn’t make it an ideal precursor.

The DNA packaging of eukaryotes consists of eight histones (proteins) in short cylinders organized into nucleosomes, which are assembled like beads on a string, then compacted into the cell nucleus. Archaea also package their DNA but coil their DNA in a completely different manner like a slinky.

A research team at the University of Colorado, Boulder and Howard Hughes Medical Institute used a cryo-electron microscope to probe how the archaeal DNA is packed. This technology can show detail at 10-billionth of a meter or less.

The work is published in the journal eLife, March 2. 

Current Science Daily talked with Karolin Luger, Ph. D., a biochemist at Howard Hughes Medical Institute and the University of Colorado, and one of the paper's authors.

Luger said that the research team was looking at primitive bacteria and archaea to find clues about how the chromosome packaging system of more complex organisms may have evolved.

Archaea are unicellular organisms that "became famous," she said, "because they grow in really insane environments —100-degree C temperatures, sulfuric acid, or Yellowstone hot springs, for example."

"But some strains also grown on our skin, in soil, and everywhere. It turns out that archaea probably invented the nucleosome, the DNA packaging structure in eukaryotes," she said.

"Archaea already have a precursor to the little tiny spools that we use to organize our DNA, but they are much simpler," Luger said. "We were looking for a primitive simplified version. Rather than form structures that look like beads on a string, archaea just form a slinky shape, where longer oligomers and proteins wrap the DNA around the outside."

"We called it a slinky when we published our first paper in 2017, but we didn't have the proof. In this new paper, we have conclusive proof that it is really a floppy slinky," she said.

"This serves the archaea really well," Luger said. "They have tiny genomes, and they don't need to do much regulation."

An evolutionary precursor

"One theory for how eukaryotes came to be is that one archaea ate a bacterium and they fused together, and that archaea-bacteria became the nucleus," she said. "It brought to the table histones, and many other activities that deal with DNA."

Luger speculates that the way the slinky shape bends and can open like a book could be designed to give archaeal proteins access to the genes in the DNA.

Luger noted other differences between eukaryote and the more primitive archaea chromatin. 

"We have four distinct histones that make up the proteins, but archaea just have one," she said. "Why do it with four, if you can do it with one? Archaea need to be quite conservative, because they need to replicate rapidly. So they need to keep their genome small." 

Luger emphasized that "the more profound difference is the ability to form these more extended slinky like structures rather than defined beads on a string of particles."

CryoEM technology

Earlier experiments by the research group used X-ray crystallography to deduce the archaeal DNA structure. The current work used a newer technology: cryo-electron microscopy, a technological advance which recently won a Nobel Prize for its developers. 

"This method is a super-powerful microscope," Luger said. "You don't have to form crystal lattices anymore, the way we did with X-ray crystallography, because that sometimes can become time consuming and often doesn't work."

"With cryoEM, you put your sample on a grid and the holes in the grid will generate a very thin water film containing the protein to be investigated. Then you freeze it extremely rapidly so it's vitrified. It doesn't form ice, but it forms a vitrified structure in which your little particles are embedded in all kinds of different orientations. Then you look at them under a microscope," she said.

"It's fabulous," Luger said. "We used this approach for our second paper, because it allowed us to possibly get structures of more structural states, and to see our structure in different arrangements. "Whichever way they open up, we can group the particles in different classes--closed, open, half-open. If we are lucky, we can actually see individual atoms and water molecules, although for this particular project that wasn’t possible." 

The only problem with the cryo-EM technology is the expense. The machine that the Howard Hughes Medical Institute bought for $8 million requires a dedicated staff person and has a service contract that costs hundreds of thousands of dollars a year, Luger said. 

"It's a powerful method, but not accessible for smaller institutions," Luger said. "People shouldn't be limited in the kinds of things they're doing by where they are, so we opened a center to which people can send their samples for research and apply for time with a fee. This is part of an effort to bring the technology to the general research public."

What's next for archaea research?

Current Science Daily asked Luger about the future of the team's research.

"We're really interested in archaea that live at extreme conditions," she said. "Because it's all chemistry. If you have an organism that lives at boiling temperatures in sulfuric acid, how have they evolved to maintain their genome and function under these conditions?"

Luger stressed the importance of pointing out to people who are concerned with the practical applications of research for curing disease "that all of our major breakthroughs in science have come from studying really weird things. For example, the discovery of penicillin, fungi, finding out that they stop the growth of bacteria: How come?" 

She noted that their basic research with DNA has implications for human health. 

"My lab is doing a number of projects all centered on the organization of this thread of DNA in the nucleus, how it's made accessible, and how it's assembled and repaired," she said.

"If bad things happen to the DNA, and it gets damaged, the faulty DNA can cause cancer. So, we have one project where we work on devising better cancer drugs by understanding fundamentally how DNA repair works in this context," she said.

"This is work by people in my lab, and we often collaborate with researchers from all over the world" Luger said. “I don't do the direct research, but I have talented and dedicated hard-working folks in the lab who bring their lifeblood to the table, and they deserve all the credit." 

Luger mentioned Francesca Mattiroli and Sudipta Bhattacharayya for the crystallography, and Samuel Bowerman for the later cryoEM work.

A 90-second computer simulation of the archaeal DNA can be seen here.