People: Astrobiology Faculty

John Leigh
Microbiology

In considering possible life on other planets, surely we ought to have the broadest possible view of life on earth. The Archaea have widened our perspective in several ways. The most extreme thermophiles are Archaea, as are the extreme halophiles and some of the strictest anaerobes. Archaea thrive in intriguing habitats, such as hydrothermal vents and the subsurface biosphere. Although simple in cell structure like bacteria, molecular mechanisms are distinctive, and replication, transcription, and translation are more eukaryotic-like than bacterial. Finally, many Archaea have “unusual” metabolisms, “eating” hydrogen, sulfur, or iron, and “breathing” carbon dioxide or sulfur.

We focus on one species of Archaea, Methanococcus maripaludis. This species is a laboratory model amenable to modern genetic and molecular techniques, and as such is a “window” into the Archaea. M. maripaludis is representative of methanogenic Archaea that use hydrogen as electron donor and carbon dioxide as electron acceptor to generate energy, resulting in the production of methane as a metabolic waste product. Methanogenesis is one of several kinds of metabolism thought to have evolved early in the history of life on earth, and since methane is a greenhouse gas, may explain the moderate temperatures enjoyed by early life during the time of the faint young sun. One of our research interests addresses the mechanism of energy conservation during methanogenesis, and indications are that although it is chemiosmotic, it differs considerably from the familiar aerobic bacteria and mitochondria. If the mechanism turns out to be relatively simple, it could reflect a form of energy conservation that evolved early.

Another metabolic function that has attracted our interest is nitrogen fixation, the means by which many Bacteria and Archaea convert atmospheric nitrogen to ammonia for incorporation into proteins and other cellular constituents. A long-standing research interest is the regulation of nitrogen fixation, and M. maripaludis has proven to be a useful laboratory model for these studies. Nitrogen fixation is an energy-intensive process and the enzymes that catalyze the reactions of nitrogen fixation (nitrogenases) are present and active only when necessary. The way the regulation of nitrogen fixation is accomplished in Archaea (as revealed by M. maripaludis) has proven to be distinctive. Thus, we have discovered and characterized a uniquely archaeal protein, a repressor, that prevents expression of the genes for nitrogen fixation. In addition, we have found a novel mechanism for regulating the activity of nitrogenase, once the genes have been expressed and the enzymes made. Against this background of mechanistic diversity, we have found one feature that both Bacteria and Archaea hold in common—the use of the metabolic intermediate 2-oxoglutarate as the indicator that the cell is nitrogen-starved and needs to fix nitrogen. Phylogenetic analyses of the repressor protein and the nitrogenase inhibitor protein reveal that both represent ancient gene families.

More recently our work with M. maripaludis has been at the genomic level, and with our determination of the complete genome sequence in collaboration with Maynard Olson, we have been able to address several new questions relating to the entire set of cellular processes. We have identified genes involved in redox metabolism whose expression is increased when the cell becomes starved for hydrogen. Experiments to determine the mechanism of this regulation are underway. The genome sequence also allows us to study evolution, by determining the apparent lineages of genes for specific functions. For example, M. maripaludis is the only species of Archaea known to use alanine as a nitrogen source. It turns out that this capability appeared in an ancestor of M. maripaludis when it acquired the necessary genes by lateral transfer from a member of the Gram positive bacteria. Another project based on the genomic sequence is to determine the minimal set of genes that is essential for viability and growth.

Leigh Lab

Publications

Lie, T. J., G. E. Wood, and J. A. Leigh. 2005. Regulation of nif expression in Methanococcus maripaludis: Roles of the euryarchaeal repressor NrpR, 2-oxoglutarate, and two operators. J. Biol. Chem. 280:5236-5241.

Dodsworth, J. A. and J. A. Leigh. 2006. Regulation of nitrogenase by 2-oxoglutarate-reversible, direct binding of a PII-like nitrogen sensor protein to dinitrogenase. Proc. Natl. Acad. Sci. USA 103:9779-9784.

Hendrickson, E. L., A. K. Haydock, B. C. Moore, W. B. Whitman, and J. A. Leigh. 2007. Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea. Proc. Natl. Acad. Sci. USA 104:8930-8934.

Hendrickson, E. L., and J. A. Leigh. 2008. Roles of coenzyme F420-reducing hydrogenases and hydrogen- and F420-dependent methylenetetrahydromethanopterin dehydrogenases in reduction of F420 and production of hydrogen during methanogenesis. J. Bacteriol. 190:4818-4821.