Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea

Abstract

Nitrosomonas europaea uses only NH(3), CO(2) and mineral salts for growth and as such it is an obligate chemo-lithoautotroph. The oxidation of NH(3) is a two-step process catalyzed by ammonia monooxygenase (AMO) and hydroxylamine oxidoreductase (HAO). AMO catalyzes the oxidation of NH(3) to NH(2)OH and HAO catalyzes the oxidation of NH(2)OH to NO(2)(-). AMO is a membrane-bound enzyme composed of three subunits. HAO is located in the periplasm and is a homotrimer with each subunit containing eight c-type hemes. The electron flow from HAO is channeled through cytochrome c(554) to cytochrome c(m552), where it is partitioned for further utilization. Among the ammonia-oxidizing bacteria, the genes for AMO, these cytochromes, and HAO are present in up to three highly similar copies. Mutants with mutations in the copies of amoCAB and hao in N. europaea have been isolated. All of the amoCAB and hao gene copies are functional. N. europaea was selected by the United States Department of Energy for a whole-genome sequencing project. In this article, we review recent research on the molecular biology and biochemistry of NH(3) oxidation in nitrifiers.

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“…Figure 5a indicated that NH 2 OH 45 mg l À 1 completely inhibited phenol degradation, whereas 50 mg l À 1 NO 2 À did not inhibit phenol degradation. Both ammonia-oxidising Archaea and ammonia-oxidising Bacteria oxidise NH 3 into NH 2 OH (Arp et al, 2002;Vajrala et al, 2013), which is then further oxidised to nitrite (NO 2 À ) and finally nitrate (NO 3 À ). The experimental data clearly indicated that it was NH 2 OH, but not NO 2 À , NO 3 À or NH 3 , that inhibited phenol degradation in the coking wastewater.…”

Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea

“…Recent studies have established that marine and terrestrial representatives of an abundant group of archaea, now classified as Thaumarchaeota, are autotrophic NH 3 oxidizers (1)(2)(3)(4)(5). Despite increasing evidence that ammonia-oxidizing archaea (AOA) generally outnumber ammonia-oxidizing bacteria (AOB), and likely nitrify in most natural environments, very little is known about their physiology or supporting biochemistry (6,7). Genome sequence analyses have pointed to a unique pathway for NH 3 oxidation, likely using copper as a major redox active metal, and coupled to a variant of the hydroxypropionate/ hydroxybutyrate cycle (8).…”

“…NH 2 OH is subsequently oxidized to NO 2 − by the hydroxylamine oxidoreductase (HAO) (7), a heme-rich enzyme encoded by the hao gene (7). Of the four electrons released from the oxidation of NH 2 OH to NO 2 − , two are transferred to the terminal oxidase for respiratory purposes and two are transferred to AMO for further oxidation of NH 3 (7).…”

“…NH 2 OH is subsequently oxidized to NO 2 − by the hydroxylamine oxidoreductase (HAO) (7), a heme-rich enzyme encoded by the hao gene (7). Of the four electrons released from the oxidation of NH 2 OH to NO 2 − , two are transferred to the terminal oxidase for respiratory purposes and two are transferred to AMO for further oxidation of NH 3 (7). Although all available genome sequences for the AOA contain homologs of the bacterial AMO (amoB, amoC, and amoA), there are no obvious homologs of AOB-like HAO, or cytochromes c554 and c M 552 critical for energy conversion in AOB (8)(9)(10)(11)(12)(13)(14)(15).…”

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“…It is possible that the different groups of AOAs prefer environments with different amounts of ammonium, e.g., open ocean, marine water columns, where typical ammonium concentrations are <0.03~1 μM (Konneke et al, 2005;Wuchter et al, 2006;, Beman et al, 2008) are dominated by Group 1.1a, while Group 1.1b are found in many Nrich environments, e.g., bioreactors and agricultural soils. Furthermore, increased amoA expression by AOAs has been found in soils after addition of 10 mM NH 4 Cl (Treusch et al, 2005) suggesting the expression of archaeal amoA gene, like bacterial amoA genes (Arp et al, 2002), may be induced by ammonia. Since agricultural soils and estuaries receiving agricultural run-off typically are usually reported to be higher ammonium concentrations, the ammoniaoxidizing archaea in group 1.1b lineage may have adapted to such environments, while the group 1.1a thrives in marine or oligotrophic ecosystems.…”