by Cherie Winner
 Northlight Images, Keith Cooper
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.
 Archaea resemble bacteria, but based on their DNA sequences, they are more closely related to plants and animals.
“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.
 Courtesy Cynthia Haseltine
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.
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