Unexpected Complexity of the Ammonia Monooxygenase in Archaea

Abstract

Ammonia oxidation as the first step of nitrification constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase is lacking, in particular for the environmentally abundant ammonia oxidizing archaea (AOA). Here, the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Beside the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modelling and in gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase indicating that AmoY and AmoZ serve an important structural and functional role. These data open avenues for further structure-function studies of this ecologically important key nitrification complex.

The effect of methane and methanol on the terrestrial ammonia‐oxidizing archaeon ‘Candidatus Nitrosocosmicus franklandus C13’

“…Interestingly, methane and methanol did not significantly affect the expression of the subunits of AMO in the proteome. Whilst there was a consistent pattern in the expression of all subunits, including the recently identified subunits AmoX, AmoY and AmoZ (Hodgskiss et al, 2022), the differences between cultures grown with and without C1 compounds were not statistically significant (Figure S4). Contrary to our expectations, there was a significant upregulation of the urease enzyme subunits UreA, UreB and UreC in response to methane.…”

Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite- oxidizing strains

“…Previous culture-based studies on the sensitivity of AOM to SNIs and BNIs have shown a rather selective inhibition of AOB by SNIs (Papadopoulou et al, 2020;Shen et al 2013;Taylor et al 2013) and a stronger inhibition of AOA by BNIs (Kaur-Bhambra et al 2022). The variable sensitivity of soil AOM to different NIs may arise from fundamental differences in their biochemistry and physiology (Hodgskiss et al, 2023;Schleper and Nicol, 2010) and could be related to the particular mode of action of each NI at cellular level with some of them (e.g., simvastatin)…”