Transformations of Dimethylsulfide - The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment - page 295

Aquificales (mostly Sulfurihydrogenibium sp.), and some species of -Proteobacteria

(e.g., Sulfuricurvum ) is located on a separate branch close to the core DMS dehydro-
genase group.
The finding of Ddh homologues in Sagittula stellata is interesting due to the
reported ability of the organism to oxidize DMS to DMSO under aerobic conditions
[ 62 ], providing an auxiliary energy source to the organism during heterotrophic
growth [ 19 ]. However, a DMSDH enzyme assay of biomass grown on succinate
and DMS was negative for the activity and SDS-PAGE analysis did not show
obvious induction of Ddh subunits in the presence of DMS [ 19 ]. It is possible that a
different enzyme system is responsible for oxidation of DMS to DMSO in this
organism during aerobic heterotrophic growth and the role of the Ddh homologues
and the conditions for their expression still need to be determined in S. stellata .
The DdhA-homologous sequences derived from the above organisms have ~40 %
aa sequence identity to DdhA and the other two subunits are not as well conserved as
in the first cluster of sequences. Despite this, these enzymes may still represent DMS
dehydrogenases although the annotation of these sequences varies and mostly reflects
their status as uncharacterized proteins. Experimental evidence will be required
to determine the function of the encoded enzymes.

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2.3 Phylogeny of Dimethylsulfoxide Reductases
and Dimethylsulfide Dehydrogenases

As briefly set out above, within the DMSO reductase enzyme family at least
three subgroups of enzymes have been identified using phylogenetic analyses of the
amino acid sequences of the catalytic subunits. Type I enzymes are the formate
dehydrogenase/Nap-type nitrate reductase enzymes, Type II enzymes are the function-
ally most diverse group and encompass DMS dehydrogenase, Nar-type nitrate
reductase, ethylbenzene dehydrogenase, and related enzymes while the soluble
DMSO/TMAO reductases (Dor-type) are classified as Type III enzymes [ 79 , 175 , 180 ].
An alternative way of classifying the enzymes in this enzyme family is to group
them according to the nature of the amino acid ligand present at the Mo center, or
based on the substrate/type of reaction catalyzed. The Mo centers of the DMSO
reductase family enzymes fall into three broad categories using this classification
method - Mo centers with a serine ligand (DMSO/TMAO reductases), Mo centers
with Cys or SeCys ligands (formate dehydrogenases, Nap-type nitrate reductases),
and with an Asp ligand (ethylbenzene dehydrogenases, Nar-type nitrate reductases)
[ 84 ]. There is some evidence for the existence of a fourth group of enzymes,
currently exemplified by the Aio arsenite oxidase, that completely lacks an amino
acid ligand to the Mo center [ 87 , 181 ].
With the exception of this arsenite oxidase, the groupings identified using the
amino acid ligand to the Mo center correspond to the phylogenetic groups identified
by McDevitt et al. [ 175 ] with the Type I enzymes having Cys or SeCys ligands, the
Type II enzymes having an aspartate ligand to the Mo center and the Type III
enzyme having a serine ligand.