The Consortium for Archaeal Genomics and Proteomics has been established at Penn State under the leadership of James G. Ferry with support from the National Science Foundation, anticipated to exceed $1.3-million over the next four years. The consortium will research the structure and function of the genes and proteins of organisms classified in the Archaea--the grouping that is thought to include the organisms living today with the most ancient evolutionary lineages.
Of the three domains in which living things are classified, the Archaea domain is likely the least familiar to most people--but Ferry and his research team aim to make it much more well known to scientists by revealing many of its secrets. Unlike organisms in the other two domains--the Bacteria and the Eucarya, which include plants, animals, fungi, algae, and other familiar organisms--the Archaea domain includes exotic forms of bacteria that live in extreme environments such as hot springs and salt lakes.
"Our efforts are expected to greatly expand the knowledge of novel biochemical and molecular biological characteristics of the Archaea, some of which are totally unique while others are a blend that appears to be 'borrowed' from both the Bacteria and Eucarya," Ferry says. The consortium's results are expected to contribute to a fundamental understanding of the Bacteria and Eucarya domains, as well.
The consortium is a collaborative research effort lead by Penn State that includes researchers at the Whitehead/Massachusetts Institute of Technology Institute for Genomic Research, the University of the City of Los Angeles (UCLA), and the University of Maryland Center for Marine Biotechnology.
The model organism chosen for the project was first discovered by Ferry's laboratory living in oxygen-starved marine sediments from the Scripps canyon near La Jolla Shores in California. This species, named Methanosarcina acetivorans, ranks as the most metabolically diverse of all the Archaea because it has the largest genome yet sequenced from an Archaea organism--4.5 million base pairs.
"Our basic approach is to exploit this genomic sequence through the use of DNA microarrays to identify the genes that are regulated in response to environmental changes," Ferry explains. Researchers in the consortium also plan to supplement this approach with genetic and bioinformatic techniques used in genomics research and with enzyme techniques used in proteomics research. The consortium's research on proteins is an outgrowth of the NSF-funded Penn State Center for Microbial Structural Biology, which Ferry also directs. Daniel Jones, a senior scientist and the director of the Penn State Mass Spectroscopy Facility, will assist consortium researchers in their studies of cellular proteins with the analysis of two-dimensional gel-electrophoresis patterns.
"By exploring the metabolic diversity of our model organism we hope to discover novel enzymes and proteins with potential uses in biotechnology," Ferry says. The consortium's model organism and others like it, which produce methane, are ancient microbes whose direct ancestors are thought to have evolved at the time of the origin of life. "One expected outcome of the project is a more thorough understanding of the origin and early evolution of life--a goal that dovetails with those of the Penn State Center for Astrobiology, of which our lab is a member," Ferry comments. "In addition, anaerobic microbial food chains are essential links in the global carbon cycle, annually producing nearly a billion tons of methane--a potent greenhouse gas--so a better understanding of this process will have global environmental significance."
PHOTOS: Reporters may obtain a high-resolution image of the Methanosarcina acetivorans organism that the researchers will study from a link at