The first look at how archaea package their DNA reveals they’re a lot like us

Single-celled microbes may have taught plants and animals how to pack their genetic baggage.

Archaea, a type of single-celled life-form similar to bacteria, keep their DNA wrapped around proteins much in the same way as more complex organisms, researchers report in the Aug. 11 Science. This finding provides new insight into the evolutionary origins of the DNA-packing process and the secret to archaea’s hardiness, which enables some to live in acid, boiling water or other extreme environments.
All eukaryotes, including plants and animals, store their genetic material in cell compartments called nuclei. Such organisms cram meters of genetic material into the tiny nuclei by wrapping strands of DNA around clusters of proteins called histones (SN: 1/10/15, p. 32). “It doesn’t really matter which eukaryote you look at, whether it’s amoebas or plants or humans or fish or insects or anything,” says coauthor John Reeve, a microbiologist at Ohio State University. “They all have exactly the same structure.”

Unlike bacteria, some archaea also contain histones, but researchers weren’t sure whether these microbes spool DNA around the protein bobbins the way eukaryotes do. So Reeve and colleagues used a method called X-ray crystallography to discern, for the first time, the precise shape of archaea DNA bound to histones.

The researchers saw that archaea DNA coils around the histones, similar to the way it does in eukaryotes. “It’s a big deal actually seeing this,” says Steven Henikoff, a molecular biologist at the Fred Hutchinson Cancer Research Center in Seattle who was not involved in the work. The resemblance between archaea and eukaryote DNA wrapping means that the first organism that used this storage scheme was an ancestor of both modern eukaryotes and archaea, the researchers conclude.

But the way archaea DNA twists around histones isn’t identical to the coils of DNA seen in eukaryotes. In eukaryotes, a strand of DNA loops twice around a cluster of eight histones to create what’s called a nucleosome, and connects many of these nucleosomes like beads on a string. Archaea DNA string together bundles of proteins, too. But while eukaryotes always tether eight-protein clumps, archaea DNA can spiral around stacks of many more histones to create rod-shaped structures of various lengths. “So it’s not as uniform as in eukaryotes,” says coauthor Karolin Luger, a biophysicist and Howard Hughes Medical Institute investigator at the University of Colorado Boulder.

Researchers tested the importance of that rodlike architecture by tampering with the histone-DNA structures of some archaea and then observing how these mutant archaea fared in different conditions. “We tried to mimic some real-life situations that some of these organisms could get into,” Luger says.
For instance, some archaea that live in volcanic vents that emit sulfurous gases sometimes get spewed out and have to survive sans sulfur. Archaea with normal histone-DNA shapes can handle that kind of midlife crisis. But when researchers cut their mutant microbes off sulfur, the microorganisms’ growth was stunted. These microbes may not have been able to adapt to sulfur deprivation as well as their wild counterparts “because they can’t unpackage their DNA as readily if the structure has been changed,” Reeve says.

Henikoff calls it “a pretty cool experiment.” It showed that the archaea’s particular DNA-histone architecture was “biologically relevant, not just a novelty,” he says.