The nitrogenase cofactor biogenesis enzyme NifB is essential for the viability of methanogens

Abstract

Dinitrogen (N2) is only bioavailable to select bacteria and archaea that possess the metalloenzyme nitrogenase, which reduces N2 to NH3 in a process called nitrogen fixation or diazotrophy. A long-term goal is to engineer diazotrophy into plants to decrease the use of nitrogen fertilizers, saving billions of dollars annually and greatly reducing nutrient pollution. This goal has not been realized, in part due to the inability to produce the nitrogenase metallocofactor within plants. Biogenesis of the cofactor requires NifB, a radical S-adenosy-L-methionine (SAM) enzyme that generates a precursor [8Fe-9S-C] cluster that matures into the final metallocofactor. Although maturation of nitrogenase is the only known function of NifB in bacteria, bioinformatic analyses reveal that NifB is conserved across methanogens, including those lacking nitrogenase, which suggests NifB functions outside of nitrogenase maturation. Indeed, several lines of evidence show that NifB is essential for viability of the model diazotroph, Methanosarcina acetivorans. First, CRISPRi repression was unable to abolish NifB production, whereas CRISPRi repression abolishes non-essential nitrogenase production. Second, unlike nitrogenase production, NifB production is not controlled by fixed nitrogen availability. Finally, nifB could not be deleted from M. acetivorans unless complemented in trans with nifB from other methanogens, including Methanothrix thermoacetophila, a species that lacks nitrogenase. Notably, M. thermoacetophila NifB supported diazotrophy in M. acetivorans, demonstrating that NifB from a non-diazotrophic methanogen produces the [8Fe-9S-C] cluster. Overall, these results link the metallocofactor biogenesis function of NifB to nitrogen fixation and methanogenesis, two processes of global importance. SIGNIFICANCEMethanogens directly impact life on Earth since they produce methane, a potent greenhouse gas, and are the principal archaea capable of nitrogen fixation, a process that requires nitrogenase. In this study, we demonstrate that NifB, an enzyme required to produce the metallocofactor in non-essential nitrogenase, is essential to the viability of methanogens. This identifies NifB as a new potential target in the goal of inhibiting methanogens to reduce methane emissions. The discovery that NifB functions outside of nitrogenase maturation will also aid efforts to engineer nitrogen fixation in plants, since NifB is a key factor to achieve this goal. Realization of these goals would have immense economic, environmental, and societal benefits.