Carol S. Giometti¹, Sandra L. Tollaksen¹, Xiaoli Liang¹ , Michael W. W. Adams², James F. Holden², Angeli Menon², Gerti Schut², Claudia I. Reich³, Gary J. Olsen³, and John Yates, III^4 
1Center for Mechanistic Biology and Biotechnology, Argonne National Laboratory, Argonne, IL 60439; ²Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229; ³Department of Microbiology, University of Illinois, Urbana, IL 61801; and ⁴Department of Molecular Biotechnology, University of Washington, Seattle, WA 98195-7730 
csgiometti@anl.gov 

The genomes of several Archaea are either partially or completely sequenced, revealing the presumptive sequences of encoded proteins. However, the functions of these proteins can only be inferred from sequence similarity with known proteins, and the mechanisms by which the expression and function of most of the proteins are regulated remain unknown. The goal of the Archaeal Proteomics Project is to identify archaeal proteins and regulatory pathways relevant to bioremediation and energy technology, processes of interest to the U.S. Department of Energy. We are using two-dimensional gel electrophoresis (2DE) to purify and quantitate proteins expressed in Archaea grown under a variety of conditions designed to modulate specific metabolic pathways. The compartmentalization of Archaeal proteins is being determined by 2DE of subcellular fractions. Proteins are identified on the basis of similarities between observed peptide masses for tryptic digests generated from proteins in the 2DE gels and calculated peptide masses for the proteins encoded in the genome sequences. We are obtaining peptide masses by using matrix-assisted laser desorption ionization mass spectrometry. Initial work is focused on the proteomes of Pyrococcus furiosus and Methanococcus jannaschii, both hyperthermophilic Archaea with growth temperatures near 100 ^oC and enzymatic capabilities that promise to be of value in bioremediation reactions, energy conversion, and chemical processing systems. Whereas many of the enzymatic activities associated with primary metabolic pathways have been characterized in P. furiosus, the metabolic capabilities of M. jannaschii have only been inferred from gene sequence information. Thus far, the most abundant proteins in the 2DE patterns of M. jannaschii and P. furiosus lysates have been identified using peptide mass searches, membrane and cytosolic proteins from P. furiosus have been compared, and quantitative changes in M. jannaschii proteins under several different growth conditions have been analyzed. These preliminary results are the foundation for the M. jannaschii and P. furiosus proteome databases. This work is support by the U.S. Department of Energy, Office of Biological and Environmental Research, under Contract No. W-31-109-Eng-38. 

The submitted manuscript has been created by the University of Chicago as Operator of Argonne National Laboratory ('Argonne') under Contract No. W-31-109-ENG-38 with the U.S. Department of Energy. The U.S. Government retains for itself, and others acting on its behalf, a paid-up, nonexclusive, irrevocable worldwide license in said article to reproduce, prepare derivative works, distribute copies to the public, and perform publicly and display publicly, by or on behalf of the Government.