Living on hydrazine: Metabolic protein complexes from an anaerobic ammonium oxidizer.

Abstract

The discovery of anammox bacteria in the 1990s has dramatically changed our understanding of the global nitrogen cycle. Anammox bacteria are now believed to be responsible for up to 30 to 70% of the nitrogen removal from the oceans. These organisms have the unique metabolic ability to combine ammonium and nitrite to form dinitrogen gas, a process that takes place in a special cellular compartment, the anammoxosome. To elucidate how bacteria perform such extraordinary chemistry, we have determined the structures of the key enzymes in this process. Central to harvesting the energy from hydrazine is the hydrazine dehydrogenase (HDH), which converts hydrazine into dinitrogen gas, liberating four extremely low-potential electrons (−750 mV). Our crystal and cryo-EM structures reveal that this 1.7-MDa complex contains an extended system of 192 heme groups spanning the entire complex, which is only accessible via narrow holes in the side of the complex. Moreover, we identified an unexpected assembly factor for this complex. In addition, anammox bacteria obtain additional reducing equivalents through the oxidation of nitrite to nitrate, which is catalyzed by a nitrite oxidoreductase (NXR) related to the NXR from nitrifying bacteria. Despite its importance in the biogeochemical nitrogen cycle, essential issues on NXR functions remain unanswered, particularly due to the lack of structural information. To meet this challenge, we used a multiscale approach combining cryo-electron tomography, crystallography, single-particle cryo-EM together with reconstitution studies and enzyme kinetics to characterize NXR. We show that, in contrast to what was shown for NXR in NOB, NXR of anammox bacteria forms tubule-like structures inside the anammoxosome held together by a novel subunit NXR-T. As with the hydrazine dehydrogenase structure, our multiscale structure of the anammox NXR tubules suggest how electrons are passed on to redox partners.