Our research is centered on methanogenic archaea ("methanogens"), ancient microorganisms that comprise the largest and most diverse group of organisms within the archaeal domain of life. Their sole source of energy is methanogenesis, a form of anaerobic respiration that reduces simple oxidized carbon compounds to generate methane as an end product. Methanogenesis generates over a billion tons of methane each year, which accounts for ~70% of global methane emissions. Given that methane is a potent greenhouse gas as well as a useful energy source, understanding methanogenic metabolism is an important endeavor that could lead to methane mitigation strategies and support bioenergy technologies. Methanogens contain a wealth of unusual biochemistry, much of which remains to be discovered or fully understood. My lab seeks to uncover and characterize novel enzymes, reactions, and biomolecules in methanogens. We are specifically interested in radical SAM enzymes in methanogens as well as the role of coenzyme F430 modifications in the methyl-coenzyme M reductase reaction.
Determining the functions and biosynthesis of coenzyme F430 modifications
Coenzyme F430 is a nickel-containing tetrapyrrole that is required for the final step of methanogenesis and the first step of anaerobic methane oxidation catalyzed by methyl-coenzyme M reductase (MCR). We recently discovered a modified version of coenzyme F430 denoted F430-3. The proposed structure of F430-3 contains a cyclized 3-mercaptopropionate moiety bound as a thioether. Interestingly, this is structurally similar to the only other previously described modified F430 that is found in archaea performing anaerobic oxidation of methane via reverse methanogenesis. We propose that F430 modifications are involved in fine-tuning the MCR active site to enhance catalytic efficiency, influence dynamics and stability, and/or to guide the directionality of the MCR reaction. Current research is focused on demonstrating the function of F430-3 using genetic, physiological, and biochemical studies. We are also investigating the enzymes involved in the biosynthesis of F430 modifications.
Compatible solute biosynthesis
In order to cope with salt stress in high salinity environments, organisms must accumulate ions or organic compounds inside the cell in order to keep water from leaving the cell via osmosis. The organic compounds used for this function are known as osmolytes or compatible solutes. The major compatible solutes in methanogens are N-acetyl-beta-lysine and beta-glutamate. In N-acetyl-beta-lysine biosynthesis, alpha-lysine is converted to beta-lysine by lysine-2,3-aminomutase (KAM), a member of the radical S-adenosyl-L-methionine (SAM) superfamily. Radical SAM enzymes catalyze diverse and complicated radical-mediated chemistry using a [4Fe-4S] cluster and SAM. beta-glutamate, another compatible solute in methanogens, is likely also generated via radical SAM dependent chemistry. We are currently working to characterize the KAM enzymes from methanogens and to identify and characterize the enzyme responsible for beta-glutamate synthesis.
Methylated pterin biosynthesis
Methanopterin is a one-carbon (C1) carrier coenzyme present in methanogens that is structurally and functionally similar to folate, the more common C1 transfer coenzyme. One difference in the structure of methanopterin compared to folate is the presence of two methyl groups at the C-7 and C-9 positions of the pterin. We have identified a single radical SAM enzyme from Methanocaldococcus jannaschii that catalyzes the addition of both methyl groups to a pterin-containing precursor. Interestingly, this methylase does not use SAM as a methyl group donor and thus is the founding member of a new class of radical SAM methylases. Our current work is focused on uncovering the mechanism of action of this enzyme and related enzymes in other methanogenic species.
We are grateful to the NSF (NSF-CHE 2105598) and DOE (DE-SC0022338) for funding our research.