Program Focus


Research in my lab is centered on methanogenic archaea, a diverse group of anaerobic microorganisms with a complex energy metabolism dependent on one-carbon biochemistry to reduce CO2, formate, methyl compounds, and/or acetate to produce methane as a final end product. This process, called methanogenesis, generates over a billion tons of methane each year, which accounts for >70% of the methane generated on Earth. Given that methane is a potent greenhouse gas as well as a great energy source, understanding methanogenic metabolism is an important endeavor. Methanogens contain a wealth of unusual biochemistry, much of which remains to be discovered or fully understood. My lab seeks to uncover and characterize new enzymes, reactions, and biomolecules in methanogens.


Current Projects


F430-3 function and biosynthesis

Coenzyme F430 is a unique nickel-containing tetrapyrrole that is required for the final step of methanogenesis 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. This is structurally similar to the only other described modified F430 that is found in archaea performing anaerobic oxidation of methane via reverse methanogenesis. We hypothesize that F430-3 tunes MCR to oxidize methane in methanogens. This is a highly desirable reaction for the possible generation of liquid fuels from methane using biocatalysis rather than inefficient chemical processes. Therefore, current research is focused on demonstrating the role/function of F430-3 as well as the genes/enzymes involved in its biosynthesis.


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-b-lysine and b-glutamate. In N-acetyl-b-lysine biosynthesis, b-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. b-glutamate is likely also generated via radical SAM dependent chemistry. We are currently working to characterize the KAM enzymes from methanogens and to determine the enzyme responsible for b-glutamate synthesis.


Methylated pterin biosynthesis

Methanopterin is a one-carbon group (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 when expressed in E. coli. We are now working to purify and understand the mechanism utilized by this new radical SAM methylase.

We are also working on a collaborative project (Fuqua Lab, Indiana University Bloomington) to determine and characterize the enzymes involved in the biosynthesis of a newly discovered methylated monapterin involved in a pathway for biofilm regulation in bacteria. 

© 2018 by Kylie Allen

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