Why Sequence the Pompeii Worm?

One of the most thermophilic eukaryotes, Alvinella pompejana, the Pompeii worm, is a resident of the Pacific deep-sea hydrothermal vent area. These worms reside on black smoker chimneys 2500 meters under the ocean surface where they experience (1) the highest temperatures and temperature gradients known for any eukaryote (20-80°C), (2) a toxic soup of heavy metals, and (3) very low pH. Thus their environment is perhaps the most extreme known for any eukaryote. This project unites cDNA sequencing, which is crucial for genetic and protein analysis, with macromolecular structure determination by x-ray crystallography, solution small-angle x-ray scattering, and electron microscopy. Proteins from thermophilic sources, currently limited to unicellular bacteria and archaea, have proven to be quite stable and amenable to the latter types of biophysical characterizations. However, bacteria and archaea are missing homologs of human proteins involved in regulation of the cell cycle, the immune system, and other systems involved in human disease. Therefore, the ability to utilize thermophilic homologs to study the structural biology of proteins immediately relevant to human disease, such as cancer, is currently compromised. Researchers have already demonstrated the utility of A. pompejana protein with a very high resolution (1.03 Å) structure of superoxide dismutase, a protein involved in Lou Gehrig’s disease, generated from cDNA. A. pompejana proteins will provide a means to address the experimental challenges emerging from interpretations of dynamic protein complexes by standing in for the human and multicellular eukaryotic proteins that have proven difficult to characterize structurally. The knowledge will benefit not only structural proteomics but also drug design and unique biological applications requiring thermostable proteins, such as in-vitro transcription and translation systems. The work may also benefit researchers in bioinformatics, biodiversity, biocomplexity, ocean ecology, adaptation and evolution, and development, as well as the study of annelids.

CSP project participants: John A. Tainer (proposer) and David S. Shin (Scripps Research Inst.), S. Craig Cary (Univ. of Delaware), and Andy Berglund (Univ. of Oregon).