Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea

Bennett, K. C.; Sadler, Natalie; Wright, Aaron; Yeager, Chris M.; Hyman, Michael R.

doi:10.1128/aem.03556-15

Cited by 41 publications

(42 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Phenylacetylene is an irreversible inhibitor of AMO from N. europaea (41,46). Here we demonstrate that phenylacetylene does not compete with NH 3 for the same binding site (Fig.…”

Section: The Inhibition Of Amo By Phenylacetylenesupporting

confidence: 50%

See 1 more Smart Citation

Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes

Wright

Schatteman

Crombie

et al. 2020

Appl Environ Microbiol

View full text Add to dashboard Cite

Ammonia monooxygenase (AMO) is a key nitrogen-transforming enzyme belonging to the same copper-dependent membrane monooxygenase family (CuMMO) as the particulate methane monooxygenase (pMMO). The AMO from ammonia-oxidizing archaea (AOA) is very divergent from both the AMO of ammonia-oxidizing bacteria (AOB) and the pMMO from methanotrophs, and little is known about the structure or substrate range of the archaeal AMO. This study compares inhibition by C2 to C8 linear 1-alkynes of AMO from two phylogenetically distinct strains of AOA, “Candidatus Nitrosocosmicus franklandus” C13 and “Candidatus Nitrosotalea sinensis” Nd2, with AMO from Nitrosomonas europaea and pMMO from Methylococcus capsulatus (Bath). An increased sensitivity of the archaeal AMO to short-chain-length alkynes (≤C5) appeared to be conserved across AOA lineages. Similarities in C2 to C8 alkyne inhibition profiles between AMO from AOA and pMMO from M. capsulatus suggested that the archaeal AMO has a narrower substrate range than N. europaea AMO. Inhibition of AMO from “Ca. Nitrosocosmicus franklandus” and N. europaea by the aromatic alkyne phenylacetylene was also investigated. Kinetic data revealed that the mechanisms by which phenylacetylene inhibits “Ca. Nitrosocosmicus franklandus” and N. europaea are different, indicating differences in the AMO active site between AOA and AOB. Phenylacetylene was found to be a specific and irreversible inhibitor of AMO from “Ca. Nitrosocosmicus franklandus,” and it does not compete with NH3 for binding at the active site. IMPORTANCE Archaeal and bacterial ammonia oxidizers (AOA and AOB, respectively) initiate nitrification by oxidizing ammonia to hydroxylamine, a reaction catalyzed by ammonia monooxygenase (AMO). AMO enzyme is difficult to purify in its active form, and its structure and biochemistry remain largely unexplored. The bacterial AMO and the closely related particulate methane monooxygenase (pMMO) have a broad range of hydrocarbon cooxidation substrates. This study provides insights into the AMO of previously unstudied archaeal genera, by comparing the response of the archaeal AMO, a bacterial AMO, and pMMO to inhibition by linear 1-alkynes and the aromatic alkyne, phenylacetylene. Reduced sensitivity to inhibition by larger alkynes suggests that the archaeal AMO has a narrower hydrocarbon substrate range than the bacterial AMO, as previously reported for other genera of AOA. Phenylacetylene inhibited the archaeal and bacterial AMOs at different thresholds and by different mechanisms of inhibition, highlighting structural differences between the two forms of monooxygenase.

show abstract

“…Phenylacetylene is an irreversible inhibitor of AMO from N. europaea (41,46). Here we demonstrate that phenylacetylene does not compete with NH 3 for the same binding site (Fig.…”

Section: The Inhibition Of Amo By Phenylacetylenesupporting

confidence: 50%

“…europaea, suggesting that the product of acetylene oxidation must bind at a different position on terminal alkynes including C 3 -C 10 1-alkynes (21), 3-hexyne (45) and 1,7-octadiyne (46).…”

Section: Downloaded Frommentioning

confidence: 99%

Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes

Wright

Schatteman

Crombie

et al. 2020

Appl Environ Microbiol

View full text Add to dashboard Cite

show abstract

“…Knowledge about the activity and structure of the enzyme ammonium monoxygenase (AMO) has been obtained mainly from studies in Nitrosomonas europaea 29 , however, it is known that the purified AMO enzyme of the heterotrophic bacterium Paracoccus denitrificans is a quinol oxidase that has similar properties to AMO enzyme from Nitrosomonas europaea and methane monoxygenase (MMO) enzyme from Methylococcus capsulatus. The amoA genes of the nitrifying heterotrophic bacteria appear to share similarities with the AOB amoA gene sequences 14 .…”

Section: Identification Of Proteins Involved In Nitrification and Denmentioning

confidence: 99%

“…T h e h y d r o x y l a m i n e o x i d a s e / hydroxylamine oxidoreductase (HAO) enzyme is a periplasmic enzyme that catalyzes the oxidation of hydroxylamine to nitrite 29 where several type C cytochromes are involved in electron transport. HAO is a key enzyme within this chain, since the electrons generated by its reaction are used by AMO who in turn generates hydroxylamine during the electron transport chain for power generation 31 .…”

Section: Identification Of Proteins Involved In Nitrification and Denmentioning

confidence: 99%

Assessment of Heterotrophic Nitrification Capacity in Bacillus spp. and its Potential Application in the Removal of Nitrogen from Aquaculture Water

Mendoza¹,

Mujica²,

Cunayque³

et al. 2019

J Pure Appl Microbiol

View full text Add to dashboard Cite

The accumulation of nitrogen (-N) is a serious problem in aquaculture as it could lead to mass mortality events of the cultivated species. Chemilitotrophic nitrification is the most recognized in nitrogen removal underestimating the role of heterotrophic nitrifiers. In the present study, the heterotrophic nitrification capacity of 8 bacterial strains isolated from mangrove soil, periphyton and biofilters was evaluated. The strains were grown in heterotrophic nitrification base medium (HNM medium) with three different nitrogen sources, ammonium, nitrite or nitrate at a final concentration of 8 mg L -1 , 5 mg L -1 and 80 mg L -1 respectively. The concentration of nitrogen (-N) and OD (600 nm) were determined periodically. Only in 4 strains belonging to the Bacillus genus was the capacity for heterotrophic nitrification and aerobic denitrification observed. Among these strains, SM4 strain presented a good removal profile of ammonium, nitrite and nitrate, achieving an average nitrification efficiency of 98. 33 ± 2.89%, 83.67 ± 7.51% and 98.00 ± 0.01% respectively, and a nitrification rate (mg L -1 h -1 ) of 1.71 ± 0.70, 0.13 ± 0.07 and 0.21 ± 0.06 respectively. The nxrB, nirS, nirK genes in the selected strains were identified by PCR. Additionally, several proteins (enzymes) involved in the nitrogen cycle were identified by proteomic analysis, reporting for the first time the presence of the enzymes ammonia monoxygenase (AMO) and nitrite oxide reductase (NXR) in the genus Bacillus. These findings suggest that the strains studied would have a potential use in the biological removal of nitrogen in aquaculture systems.

show abstract

“…Also, like host-associated communities, environmental communities have seen limited application of ABPP. ABPP has been used to study axenic cultures of environmental microbes such as nitrifying bacteria, extremophilic archaea, and cellulolytic bacteria (Chauvigne-Hines et al 2012; Bennett et al 2016; Zweerink et al 2017; Sadler et al 2014; Ansong et al 2014). Because ABPP does not require the ability to genetically manipulate organisms or the use of antibodies, it may prove especially useful in the study of microbial communities where those tools are often not available.…”

Section: Biological Applications For Abppmentioning

confidence: 99%

Activity-Based Protein Profiling—Enabling Multimodal Functional Studies of Microbial Communities

Whidbey

Wright

2018

Current Topics in Microbiology and Immunology

Self Cite

View full text Add to dashboard Cite

Microorganisms living in community are critical to life on Earth, playing numerous and profound roles in the environment and human and animal health. Though their essentiality to life is clear, the mechanistic underpinnings of community structure, interactions, and functions are largely unexplored and in need of function-dependent technologies to unravel the mysteries. Activity-based protein profiling offers unprecedented molecular-level characterization of functions within microbial communities and provides an avenue to determine how external exposures result in functional alterations to microbiomes. Herein, we illuminate the current state and prospective contributions of ABPP as it relates to microbial communities. We provide details on the design, development, and validation of probes, challenges associated with probing in complex microbial communities, provide some specific examples of the biological applications of ABPP in microbes and microbial communities, and highlight potential areas for development. The future of ABPP holds real promise for understanding and considerable impact in microbiome studies associated with personalized medicine, precision agriculture, veterinary health, environmental studies, and beyond.

show abstract

Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea

Cited by 41 publications

References 49 publications

Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes

Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes

Assessment of Heterotrophic Nitrification Capacity in Bacillus spp. and its Potential Application in the Removal of Nitrogen from Aquaculture Water

Activity-Based Protein Profiling—Enabling Multimodal Functional Studies of Microbial Communities

Contact Info

Product

Resources

About