Metal Enzymes in “Impossible” Microorganisms Catalyzing the Anaerobic Oxidation of Ammonium and Methane

Abstract

Ammonium and methane are inert molecules and dedicated enzymes are required to break up the N-H and C-H bonds. Until recently, only aerobic microorganisms were known to grow by the oxidation of ammonium or methane. Apart from respiration, oxygen was specifically utilized to activate the inert substrates. The presumed obligatory need for oxygen may have resisted the search for microorganisms that are capable of the anaerobic oxidation of ammonium and of methane. However extremely slowly growing, these “impossible” organisms exist and they found other means to tackle ammonium and methane. Anaerobic ammonium-oxidizing (anammox) bacteria use the oxidative power of nitric oxide (NO) by forging this molecule to ammonium, thereby making hydrazine (N₂H₄). Nitrite-dependent anaerobic methane oxidizers (N-DAMO) again take advantage of NO, but now apparently disproportionating the compound into dinitrogen and dioxygen gas. This intracellularly produced dioxygen enables N-DAMO bacteria to adopt an aerobic mechanism for methane oxidation.

Although our understanding is only emerging how hydrazine synthase and the NO dismutase act, it seems clear that reactions fully rely on metal-based catalyses known from other enzymes. Metal-dependent conversions not only hold for these key enzymes, but for most other reactions in the central catabolic pathways, again supported by well-studied enzymes from model organisms, but adapted to own specific needs. Remarkably, those accessory catabolic enzymes are not unique for anammox bacteria and N-DAMO. Close homologs are found in protein databases where those homologs derive from (partly) known, but in most cases unknown species that together comprise an only poorly comprehended microbial world.

Abbreviations and Definitions

ΔG ⁰′ E₀′:

Gibbs free energy changes and standard midpoint redox potentials, both at pH 7, were taken or calculated from data presented in [136, 137]

AMO:

ammonium monooxygenase

anammox:

anaerobic ammonium oxidation

AOA:

ammonium-oxidizing Archaea

AOB:

ammonium-oxidizing Bacteria

ATP:

adenosine 5′-triphosphate

bisPGD:

bis(pyrano guanine dinucleotide)

C1:

one-carbon compound

cNOR:

cytochrome c-dependent nitric oxide reductase

Cyt c :

cytochrome c

DMSO:

dimethylsulfoxide

DNRA:

dissimilatory nitrite/ nitrate reduction forming ammonium

FAD:

flavin adenine dinucleotide

Fae:

formaldehyde activating enzyme

Fhc:

formyl transferase/hydrolase

FDH:

formate dehydrogenase

FMD:

molybdenum-containing formylmethanofuran dehydrogenase

fMFR:

formylmethanofuran

fMFR-DH:

formylmethanofuran dehydrogenase

Fwd:

tungsten-containing formylmethanofuran dehydrogenase

H₄F:

5,6,7,8-tetrahydrofolate

H₄MPT:

5,6,7,8-tetrahydromethanopterin

HAO:

hydroxylamine oxidoreductase

HCO:

heme-copper oxidase

HDH/HZO:

hydrazine dehydrogenase/oxidase

HQNO:

2-heptyl hydroxyquinoline N-oxide

HZS:

hydrazine synthase

MCO:

multicopper oxidase

MDH:

methanol dehydrogenase

methanogen:

Archaeon that grows by the formation of methane

methanotroph:

organism capable of (aerobic) growth on methane

methylotroph:

organism capable of growth on methylated compound(s)

MFR:

methanofuran

MMO:

methane monooxygenase

MPT:

molybdopterin

MQ(H₂):

(reduced) menaquinone

Mtd:

methylenetetrahydromethanopterin dehydrogenase

MxaFI:

heterotetrameric calcium-containing methanol dehydrogenase

NAD(P)H:

nicotinamide adenine dinucleotide (phosphate) reduced

N-cycle:

biogeochemical nitrogen cycle

N-DAMO:

nitrite-dependent anaerobic methane oxidation

N₂OR:

nitrous oxide (N₂O) reductase

Nap:

periplasmic dissimilatory nitrate reductase

Nar:

cytoplasmic dissimilatory nitrate reductase

Nas:

assimilatory nitrate reductase

NeHAO:

Nitrosomonas europaea hydroxylamine oxidoreductase

Nir:

nitrite reductase

Nrf:

ammonium-forming nitrite reductase

NOD:

nitric oxide dismutase

NOR:

nitric oxide reductase

NXR:

nitrite:nitrate oxidoreductase

pMMO:

particulate membrane-bound methane monooxygenase

PQQ:

pyrroloquinoline quinone

qNOR:

quinol-dependent nitric oxide reductase

quinoprotein:

protein containing PQQ at its active site

REE:

rare earth element

sMMO:

soluble methane monooxygenase

tat :

twin-arginine translocation signal

TMH:

transmembrane-spanning helix

XoxF:

homodimeric rare earth element-containing methanol dehydrogenase