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Project to explore extreme organisms receives DOE funding

Friday, May 13, 2005
Written by Branwyn Wagman

Scanning electron micrograph of Pyrobaculum calidifontis, a novel hyperthermophilic archaeon that grows in atmospheric air (T. Amo, M.L.F. Paje, A. Inagaki, et al. Archaea 2002 Sept; 1(2):113–121. Reproduced by permission.)

A project to sequence the genomes of five microscopic species that grow and live in boiling hot conditions, members of the domain Archaea, has received support from the Community Sequencing Program of the Department of Energy. Two UCSC researchers, biomolecular engineer Todd Lowe and environmental toxicologist Chad Saltikov, share the project with astrobiologists Christopher House from Pennsylvania State University and Sorel Fitz-Gibbon from UCLA.

The particular Archaea being studied are three members of the genus Pyrobaculum and the closely-related species Caldivirga maquilingensis and Thermoproteus neutrophilus. Pyrobaculum species all respire toxic metals, such as arsenic and selenium, or sulfur compounds, ferric iron, nitrate, or oxygen.

Lowe says, “With these new genomes, we should be able to focus and accelerate our study of the group of genes that enable survival in one of the harshest environments inhabited on our planet." Understanding the unusually complex metabolisms of these organisms could also shed light on geological processes.

This research holds particular importance for astrobiologists, who seek to understand the wide variety of potential habitats for life. Fitz-Gibbon explains, “Studies of this group isolated from such diverse climes as terrestrial acidic hot springs and marine boiling water holes should yield tremendous progress, especially in our understanding of the mechanisms of evolution and adaptation to new environments.”

The genome of Pyrobaculum aerophilum has already been sequenced, but the species has proven difficult to grow in the laboratory. The species to be sequenced in this project are all easier to work with.

Through comparative genomics, researchers will be able to study their evolution and determine how their genes are regulated and relate to functions. These species have broad metabolic diversity, and a large proportion of their genes have not been studied in any other organisms. House adds, “I am excited that we will have a diversity of related species to study at the genomic level. In particular, our project includes related species with a variety of sulfur metabolisms."

The project includes building microarrays and genome browsers at UCSC for several of these new species to facilitate the study of their functions. According to Lowe, this allows the group to “capitalize on the local expertise in building genome browsers to share that information with the world.”

In parallel with the sequencing effort, the consortium is working on a gene knock-out system for one of the new species to be sequenced, Pyrobaculum calidifontis. Lowe says, “This will greatly simplify the characterization of many key genes that have never been studied before.”

Lowe adds, "I'm very excited that we will finally be able to bring the power of comparative genomics and traditional genetics to this metabolically agile group of hyperthermophiles.”