Leigh Lab : Research
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J o h n    L e i g h    L a b

University of Washington Department of Microbiology
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Email the Director :
John Leigh, Ph.D.


Research : Overview

Our lab studies the species Methanococcus maripaludis, a member of the methanogenic Archaea. Our fascination with this organism stems in part from its representation of the third branch of life. As microorganisms that differ from the Bacteria and the Eucaryotes, the Archaea are ripe for discovery. Within the Archaea, the methanogens are important anaerobes in a variety of habitats. Methanococcus maripaludis is a superb model because of its excellent laboratory growth behavior, a robust set of genetic tools, and a complete genome sequence.


Here are the projects going on in the lab:



Electron flow and energy conservation in methanogens

This project is driven by two overall goals. First, we want to understand the pathways of electron flow and the mechanisms of energy conservation in methanogens that lead to ATP synthesis. Second, from an applied point of view, we plan to optimize electron flow patterns to enhance the potential for methane and hydrogen production as fuels.


Hydrogen regulation and systems biology of methanogenesis

In collaboration with Nitin Baliga (Institute for Systems Biology), Murray Hackett (Department of Chemical Engineering), and William Whitman (University of Georgia), we are studying the systems biology of Methanococcus maripaludis. One important finding is that certain genes of methanogenesis are markedly increased in mRNA abundance when the culture is hydrogen-limited. We are working to find out how the organism senses hydrogen availability and how that information is transduced to control gene expression. From a broader point of view, our goal is to generate a network model of regulation in M. maripaludis. For this purpose we are currently imposing a variety of environmental and genetic perturbations and gathering data at the transcriptome, proteome, and metabolome levels. We have found that M. maripaludis grows well in chemostats, which we use to impose defined nutrient-limited conditions.


Nitrogen regulation

A wide variety of organisms sense cellular 2-oxoglutarate levels as an indicator of nitrogen starvation. Methanococcus maripaludis is no exception to this rule, as it responds to 2-oxoglutarate to regulate a variety of nitrogen assimilation functions, including nitrogen fixation. However, the components of the regulatory machinery have proven to be novel. We discovered the repressor NrpR and showed that it binds to the promoter regions of nitrogen-regulated genes, inhibiting transcription. 2-oxoglutarate acts as the inducer, preventing NrpR from binding to the DNA. We are now collaborating to obtain the tertiary and quaternary structures of NrpR and to determine how 2-oxoglutarate affects these structures. NrpR is found in a variety of Euryarchaeota but is very rare in the Bacteria and has not been found in the Eukarya.

Another novel regulator is NifI. This protein is a relative of PII proteins, which measure 2-oxoglutarate levels and interact with a variety of other proteins that regulate nitrogen assimilation functions. NifI binds directly to nitrogenase and prevents its interaction with nitrogenase reductase. We are working to determine the structural basis for the function of NifI. So far we know that it undergoes interesting quaternary changes. When 2-oxoglutarate is low NifI is a hexamer and it presumably binds as a hexamer to nitrogenase. When 2-oxoglutarate is high, NifI appears to change into a dodecamer and does not bind nitrogenase.



We are also interested in methanogenic Archaea in the context of Astrobiology. Methanogenesis probably evolved early on earth and is a likely metabolism of any life that might exist on Mars or Europa. Several members of the lab participate in the University of Washington's Astrobiology Program.

More About Methanococcus maripaludis