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the digestive breakdown of polyphenols found in seed components [33]. Each gene
cluster appears to represent a multi-component pathway, and is made up of five or
more of various combinations of dioxygenase, hydroxylase, aldolase, dehydrogenase,
hydratase, decarboxylase, and thioesterase enzymes.
The single predicted
Mhp
A protein in
D. aromatica
(VIMSS584155), which is
predicted to support an initial hydroxylation of a substituted phenol substrate, shares
64.4% identity to
Rhodococcus
OhpB 3-(2-hydroxyphenyl) propionate monooxygen-
ase (GI:8926385) versus 26.4% for
Comamonas testosteroni
(GI:5689247), yet the
remainder of the
ohp
genes in the
Rodococcus ohp
clade do not share synteny with the
D. aromatica
mhp
gene cluster.
Other Aromatic Oxygenases
Two chromosomally adjacent monooxygenase clusters, syntenic to genes found in
Burkholderia
and
Ralstonia
sp., indicate that
D. aromatica
might have broad substrate
hydroxylases that support the degradation of toluene, vinyl chlorides, and TCE (Figure
2 and Table 2), and are thus candidates for benzene-activating enzymes in the presence
of oxygen.
One monooxygenase gene cluster, composed of VIMSS581514 to 581519 (“tbc2
homologs”, Figure 2), is orthologs to the tbuA1UBVA2C/tmoAECDBF/touABCDEF/
phlKLMNOP and tbc2ABCDEF gene families (from
P. stutzeri
,
R. pickettii
, and
Bur-
kholderia
JS150). This gene cluster includes a transport protein that is orthologs to
TbuX/TodX/XylN (VIMSS581520). Specifi city for the initial monooxygenase is not
established, but phylogenetic analysis places VIMSS581514 monooxygenase with
near-neighbors TbhA [34], reported as a toluene and aliphatic carbohydrate mono-
oxygenase (76.5% sequence identity), and BmoA [35], a benzene monooxygenase of
low regiospecifi city (79.6% sequence identity). The high level of similarity to the
D.
aromatica
protein is notable. The region is also highly syntenic with, and homologous
to, the tmoAECDBF (AY552601) gene cluster responsible for
P. mendocina's
ability
to utilize toluene as a sole carbon and energy source [36].
Just downstream on the chromosome is a
phc/dmp/phh/phe/aph
-like cluster of
genes, composed of the genes VIMSS812947 and VIMSS581535 to 581540 (“tbc1
homologs”, Figure 2). Overall, chromosomal organization is somewhat different for
D. aromatica
as compared to
Ralstonia
and
Burkholderia
.
Dechloromonas
aromatica
has a 14 gene insert that encodes members of the
mhp
-like family of aromatic oxy-
genases between the tandem tbc 1 and 2-like oxygenase clusters (see Table 2), with
an inversion of the second region compared to
R. eutropha
and
Burkholderia
. Clade
analysis indicates a broad substrate phenol degradation pathway in this cluster, with
high sequence identity to the
TOM
gene cluster of
Bradyrhizobium
, which has the abil-
ity to oxidize dichloroethylene, vinyl chlorides, and TCE [37, 38]. The VIMSS581522
response regulator gene that occurs between the two identifi ed monooxygenase gene
clusters shares 50.3% identity to the
Thaurea aromatica tutB
gene and 48.2% to the
Pseudomonas
sp. Y2 styrene response regulator (occupying the same clade in phy-
logenetic analysis). The VIMSS581522 is likely to be involved in the chemotactic
response in conjunction with VIMSS581521 (histidine kinase) and VIMSS581523
