Cynthia Haseltine wants everyone to know that the microbes she works with are not bacteria.
They look like bacteria; each Sulfolobus is a single cell that has one circular chromosome and lacks a nucleus. But in their genes and the way they read and repair their DNA, these organisms bear a closer resemblance to us than to bacteria—and those similarities make Sulfolobus an excellent model system for learning about how our cells handle DNA, and how the process sometimes goes wrong.
Haseltine’s microbes belong to the group of organisms known as Archaea (ar-KAY-uh). Most Archaea are extremophiles, living in hot, saline, acidic, or other extreme environmental conditions. Sulfolobus is partial to pools hot enough to scald and as corrosive as battery acid. For years after the discovery of Archaeal species in the 1970s, scientists called them “Archaebacteria,” a name that indicated both their evolutionary age and the assumption that they were members of the bacterial clan.
“Everyone thought they were just really weird bacteria that lived in really strange places,” says Haseltine. That changed in 1996, when the first Archaeal genome sequence was published. It turned out that Archaea aren’t kin to bacteria after all. On a tree-of-life diagram based on similarity of DNA sequences, bacteria are on the left and eukaryotes, those organisms (like us) with multiple chromosomes enclosed by a nucleus, are on the right. Archaea lie in between, but closer to the eukaryotes. In other words, they’re more closely related to you and me than they are to E. coli.
Haseltine uses Sulfolobus to study DNA recombination, the essential process of swapping strands of DNA between chromosomes. Recombination occurs during DNA repair and, in eukaryotes, during the production of eggs and sperm. If something goes wrong in the process—if a cell can’t recognize the strands to be swapped, cut out the relevant sequence, or make and splice in an alternate version—death or disease results.
In eukaryotes, at least 30 proteins are needed to perform recombination. Sulfolobus accomplishes the same actions with just a handful. Haseltine compares the human system to a Cadillac and Sulfolobus to a Model T.
“They’re both cars; they both go,” she says. “[Sulfolobus] is a very, very simple one. It does exactly the same thing, just without all the fancy extras. So we’re trying to figure out how the Model T works.”
Research on Archaeal recombination proteins has already provided insights into the development of breast cancer. A few years ago a major strand-exchange protein, which helps swap a damaged section of DNA for a correct section, was isolated from an Archaean that lives near deep-sea thermal vents. When biochemists took a closer look, they found that the protein, RadA, is almost identical to a human recombination protein called Rad51. That caught the attention of researchers studying Brca2, a protein linked to the development of breast cancer. They knew that Brca2 and Rad51 worked together, but they couldn’t tell how, because Rad51 always fell apart soon after being purified. Scientists were able to use the sturdier RadA as a stand-in for Rad51 in lab tests, and solve the puzzle of how Brca2 interacts with it in the human DNA-repair system.
RadA isn’t the only Archaeal protein that’s tougher than its human counterpart. Most eukaryotic proteins must be kept cold, and even then, they can degrade within an hour of being purified. Since Sulfolobus grows in very hot conditions, its chemical components are well adapted to heat. Room temperature doesn’t faze them at all.
“You can purify a protein and put it on a shelf for four years, and it’ll be good,” says Haseltine. She points out that since Sulfolobus normally lives at 80°C, being at room temperature of 25°C is comparable to being frozen. “That’s a 55°C difference in temperature,” she says. “For E. coli growing at [human body temperature of] 37°C, a 55-degree drop puts it at minus 18°C”—well below the freezing point of water.
The downside of Archaeans’ thermal quirks is that most of the standard techniques for purifying and testing proteins were designed to run at cold temperatures. Sulfolobus proteins don’t function in the cold. Haseltine has had to adapt common lab assays to work at high temperature and low pH. So far her methods have been very successful; she’s been able to purify a number of recombination proteins from Sulfolobus and is now pursuing experiments to find out exactly how they contribute to recombination.
Haseltine is also trying to spread the word about Archaea. She understands that they’re still unknown to most people. She had never heard of them until she did a grad school rotation in an Archaeal lab. It didn’t take her long to throw in her lot with the odd organisms.
“I thought, wow, they grow in boiling acid. That is so cool! Nothing should be growing in boiling acid. Seriously! . . . I’ve never gotten away from the coolness factor.”
She says she’s seen coverage of Archaea in biology textbooks grow from a paragraph, to a paragraph plus a picture, to a few pages.
“Over time it’s gotten better,” she says. “Now we actually get three pages of a chapter. But often the instructors will skip it”—probably because they themselves don’t realize how significant Archaea are.
So far, most of the interest in Archaea has come from biotech firms quick to recognize the commercial potential of enzymes that will work under harsh conditions. The starch-digesting enzyme from Sulfolobus, for instance, was first isolated by a Japanese company that put it to work in a high-temperature beer-brewing process.
Archaea were first collected from Yellowstone hot springs, and Haseltine and her students visit the park as often as they can to collect fresh samples of Sulfolobus. They skip the sparkling blue and green pools (which have neutral or high pH) and head straight for the murkiest mudpots. “We pretty much look for anything that’s got a low pH,” she says. “Anything that smells sulfury. The pools that the public walks by and goes, ‘Eww, that’s nasty!,’ we’re like, ‘Yay! They’re going to be in there!'”
Sulfolobus‘s wide distribution—it also lives in hot pots in Italy, Iceland, Japan, and New Zealand—raises the tantalizing possibility that Haseltine could find a source right here in Washington.
“That’s one of the reasons I’m really glad to be here at WSU,” she says. “It’s a volcanic state. My bet is that within reasonable driving distance, there’s going to be hot springs here that have Sulfolobus in them”—possibly unique species that will offer new perspectives on how our cells work.