Kylie Allen

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 >90% of the methane generated on Earth. Given that methane is a potent greenhouse gas as well as a powerful 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.

Stone, S., Peters, L., Fricke, C., Ray, W. K., & Allen, K. D. (2025). Biochemical characterization of the self-sacrificing p-aminobenzoate synthase from Nitrosomonas europaea reveals key residues involved in selecting a Fe/Fe or Mn/Fe cofactor. JBIC Journal of Biological Inorganic Chemistry. DOI: 10.1007/s00775-025-02109-w

Dinh, T.-A., & Allen, K. D. (2024). Toward the Use of Methyl-Coenzyme M Reductase for Methane Bioconversion Applications. Accounts of Chemical Research. DOI: 10.1021/acs.accounts.4c00413

Polêto, M. D., Allen, K. D., & Lemkul, J. A. (2024). Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F430 Modifications. Biochemistry. DOI: 10.1021/acs.biochem.4c00168

Boswinkle, K., Dinh, T. A., & Allen, K. D. (2023). Biochemical and genetic studies define the functions of methylthiotransferases in methanogenic and methanotrophic archaea. Frontiers in Microbiology. DOI: 10.3389/fmicb.2023.1304671

Wooldridge, R., Stone, S., Pedraza, A., Ray, W. K., Helm, R. F., & Allen, K. D. (2023). The Chlamydia trachomatis p‐aminobenzoate synthase CADD is a manganese‐dependent oxygenase that uses its own amino acid residues as substrates. FEBS Letters. DOI: 10.1002/1873-3468.14573

Tunçkanat, T., Gendron, A., Sadler, Z., Neitz, A., Byquist, S., Lie, T. J., & Allen, K. D. (2022). Lysine 2,3-Aminomutase and a Newly Discovered Glutamate 2,3-Aminomutase Produce β-Amino Acids Involved in Salt Tolerance in Methanogenic Archaea. Biochemistry. DOI: 10.1021/acs.biochem.2c00014

Gendron, A., & Allen, K. (2022). Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression. Frontiers in Microbiology. DOI: 10.3389/fmicb.2022.867342

Allen, K., Wegener, G., Sublett Jr., D., Bodnar, R., Feng, X., Wendt, J., & White, R. (2021). Biogenic formation of amorphous carbon by anaerobic methanotrophs and select methanogens. Science Advances, 7(44). DOI: 10.1126/sciadv.abg9739

Macias-Orihuela, Y., Cast, T., Crawford, I., Brandecker, K., Thiaville, J., Murzin, A., de Crécy-Lagard, V., White, R., & Allen, K. (2020). An unusual route for p-aminobenzoate biosynthesis in Chlamydia trachomatis involves a probable self-sacrificing diiron oxygenase. Journal of Bacteriology. DOI: 10.1128/JB.00319-20

Labine, M., DePledge, L., Ferier, N., Greenwich, J., Fuqua, C., & Allen, K. (2020). Enzymatic and Mutational Analysis of the PruA Pteridine Reductase Involved in Pterin-Dependent Biofilm Control in Agrobacterium Tumefaciens. Journal of Bacteriology, 202, e00098-20.

White, R., Allen, K., & Wegener, G. (2019). Identification of a Redox Active Thioquinoxalinol Sulfate Compound Produced by an Anaerobic Methane-Oxidizing Microbial Consortium. ACS Omega, 4(27), 22613-22622.

Portugal, R., Shao, N., Whitman, W., Allen, K., & White, R. (2019). Identification and biosynthesis of 2-(1H-imidazol-5-yl)ethan-1-ol (histaminol) in methanogenic archaea. Microbiology, 165, 455-462.

Allen, K., & White, R. (2018). Identification of the Radical SAM Enzymes Involved in the Biosynthesis of Methanopterin and Coenzyme F420 in Methanogens. Methods in Enzymology, 606.

Allen, K., & White, R. (2016). Occurrence and biosynthesis of 3-mercaptopropionic acid in Methanocaldococcus jannaschii. FEMS Microbiology Letters, 363, fnw217.

Allen, K., Miller, D., Rauch, B., Perona, J., & White, R. (2015). Homocysteine is biosynthesized from aspartate semialdehyde and hydrogen sulfide in methanogenic archaea. Biochemistry, 54, 3129-3132.

Feirer, N., Xu, J., Allen, K., Koestler, B., Waters, C., White, R., & Fuqua, C. (2015). A Pterin-Dependent Signaling Pathway Regulates a Dual Function Diguanylate Cyclase-Phosphodiesterase Protein Controlling Surface Attachment in Agrobacterium tumefaciens. mBio, 6(4).

Hu, K., Werner, W., Allen, K., & Wang, S. (2015). Investigation of enzymatic C-P bond formation using multiple quantum HCP nuclear magnetic resonance spectroscopy. Magnetic Resonance in Chemistry, 53, 267-272.

Allen, K., & White, R. (2014). Identification of structurally diverse methanofuran coenzymes in Methanococcales that are both N-formylated and N-acetylated. Biochemistry, 53, 6199–6210.

Allen, K., & Wang, S. (2014). Spectroscopic characterization and mechanistic investigation of P-methyl transfer by a radical SAM enzyme from the marine bacterium Shewanella denitrificans OS217. Biochimica et Biophysica Acta, 1844, 2135-2144.

Allen, K., Wegner, G., & White, R. (2014). Discovery of multiple modified F430 coenzymes in methanogens and anaerobic methylotrophic archaea suggests new roles for F430 in Nature. Applied and Environmental Microbiology, 80, 6403-6412.

Allen, K., Xu, H., & White, R. (2014). Identification of a unique radical SAM methyltransferase likely involved in methanopterin biosynthesis in Methanocaldococcus jannaschii. Journal of Bacteriology, 196, 3315-3323.

Allen, K., & Wang, S. (2014). Initial Characterization of Fom3 from Streptomyces wedmorensis: The Methyltransferase in Fosfomycin Biosynthesis. Archives of Biochemistry and Biophysics, 543, 67-73.Werner, W., Allen, K., Hu, K., Helms, G., Chen, B., & Wang, S. (2011). In Vitro Phosphinate methylation by PhpK from Kitasatospora phosalacinea. Biochemistry, 50, 8986-8988.

Werner, W., Allen, K., Hu, K., Helms, G., Chen, B., & Wang, S. (2011). In Vitro Phosphinate methylation by PhpK from Kitasatospora phosalacinea. Biochemistry, 50, 8986-8988.

*Contributed equally