The effects of copper, methane and linear alcohols on archaeal ammonia oxidation

Oudova, Barbora (2023) The effects of copper, methane and linear alcohols on archaeal ammonia oxidation. Doctoral thesis, University of East Anglia.

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Abstract

Ammonia oxidising archaea (AOA) are responsible for the first step in nitrification, oxidation of ammonia to nitrite. They are ubiquitous in the biosphere where they are commonly exposed to elevated concentrations of methane and methanol. Ammonia monooxygenase (AMO), the key enzyme in the ammonia oxidation pathway, is structurally and phylogenetically similar to particulate methane monooxygenase (pMMO), which is responsible for methane oxidation in methanotrophs. While bacterial ammonia oxidisers (AOB) and methanotrophs are both capable of oxidising ammonia, methane and methanol, the substrate flexibility of archaeal ammonia oxidisers remains unknown. Copper plays an essential role in AOA, as it is the presumed cofactor of the AMO. There is limited knowledge about the copper requirements in ammonia oxidisers and the role of copper in the archaeal ammonia oxidation pathway.

Whole-cell enzyme kinetic assays performed with ‘Ca. N. franklandus’ demonstrated that both methane and methanol are competitive inhibitors of ammonia monooxygenase. There is evidence for the oxidation of methane and methanol by AMO, and the assimilation of methane and methanol-derived carbon into the archaeal biomass. There were significant changes in the expression of proteins related to stress response, metabolism of alcohols and aldehydes, the biosynthetic pathway of cofactor F420, and urease subunits. The inhibition of ammonia oxidation by ‘Ca. N. franklandus’ (AOA) and N. europaea (AOB) by alcohols (C1-C8) revealed that the AMO from ‘Ca. N. franklandus’ was specifically inhibited by C1-C2 alcohols, and the AMO from N. europaea by C1-C3 alcohols. It was demonstrated that both ammonia and hydroxylamine oxidation in AOA are copper-dependent.

These results provide evidence that AOA are important players in both the carbon and
nitrogen cycle, and insights into the metabolic pathways affected by the presence of methane and methanol in model AOA, ‘Ca. N. franklandus’. Differential responses to alcohols and the various requirements for copper contribute to our understanding of the physiology of AOA and AOB.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Nicola Veasy
Date Deposited:	11 Apr 2024 14:00
Last Modified:	11 Apr 2024 14:00
URI:	https://ueaeprints.uea.ac.uk/id/eprint/94891
DOI:

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