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The first genome sequenced by a graduate student
  
By Kate Dalke

 

As a graduate student, Sorel Fitz-Gibbon never envisioned sequencing an entire genome. Yet one doctoral thesis and many years later, she has accomplished just that.

"Hers is really the first Ph.D. thesis on the whole sequence of a genome," says Jeffrey Miller, who oversaw the research on Pyrobaculum aerophilum at the University of California, Los Angeles. Fitz-Gibbon led the entire project from the sequencing to the annotation to the resolution of the unavoidable gaps in the sequence. The project was a collaboration between the laboratories of Miller and Melvin Simon at UCLA, and findings were reported recently in Proceedings of the National Academy of Sciences.


Pyrobaculum aerophilum cell, platinum shadowed.

Progressing from the initial genome sequence to publication took years. The sequencing of P. aerophilum concluded in 1998, at which time Fitz-Gibbon defended and received her Ph.D. The researchers originally thought the genome was smaller than it turned out to be, which meant the finishing took longer than expected. Then there was the task of adding biological information to annotate the sequence.

"To piece together and annotate a sequence and to polish it well is a tremendous intellectual endeavor," Miller says.

The enormity of the project did not discourage Fitz-Gibbon, who remained optimistic throughout. "I always thought it was just a couple of months away," she says, "and it went on like that for a couple of years."

Pyrobaculum aerophilum is an extremophile, so called because it grows in extreme environments such as high temperatures or harsh chemical conditions. Karl Stetter of Regensburg University in Regensburg, Germany isolated the organism from a boiling water hole in Maronti Beach, Italy. The organism can live in temperatures up to 104 degrees Celsius (219°F). It is a member of the archaea, a third branch of life separate from both animals and bacteria.

Miller began investigating extremophiles after the US Office of Naval Research suggested researching the genetics behind high-temperature archaea. "There really was an enormous number of fundamental questions posed by these extremophiles," he says. One question is: How do these organisms live at extreme temperatures?

Answering such questions means bringing extremophiles into the laboratory, but this often presents a challenge. Many high-temperature archaea cannot tolerate oxygen, which means cumbersome and expensive anaerobic equipment is required to keep the organisms alive. Pyrobaculum aerophilum can be used in research because unlike some other archaea it can live in the presence of oxygen and can thus be worked with more freely.


Detail of phylogenetic tree of the crenarchaea. View larger

The sequencing of P. aerophilum revealed unstable runs of chemical bases that may be related to an apparent lack of a mismatch repair system in the organism. Mismatch repair is a back-up mechanism for correcting mistakes made during DNA replication. Like quality control on an assembly line, it detects and repairs the mismatch. This kind of repair is found in humans, and damage to human proteins involved in mismatch repair may predispose some people to certain types of cancer.

Whether a lack of mismatch repair genes is a feature common to P. aerophilum is not yet known. Nor is it clear why the sequenced strain has such a high rate of mutations.

The US Department of Energy provided grants for the sequencing of P. aerophilum through the Microbial Genome Project. Other DOE projects explored the structural genomics of the organism to better understand protein folding in extremophiles. The department is currently focused on microbes that have greater relevance to environmental clean-up and other DOE missions, says Daniel Drell of the Office of Biological and Environmental Research.

Fitz-Gibbon plans to continue research on the genetics of P. aerophilum. She is now a postdoctoral fellow under Bruce Runnegar at the UCLA Center for Astrobiology and the UCLA Institute of Geophysics and Planetary Physics. She continues to collaborate with Miller on a gene expression project using microarrays.

Having only six names on the research paper is an indication of how important Fitz-Gibbon was to the project. Miller says, "When word got out that this is what I required for a Ph.D. thesis, I haven't got a graduate student since."

See related GNN article
»A sequenced hyperthermophile: Pyrobaculum aerophilum

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Fitz-Gibbon, S.T. et al. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc Natl Acad Sci USA 99, 984-989 (January 22, 2002).
 

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