Biology Reference
In-Depth Information
Table 2.
(Continued)
VIMSS id
Orthologs
Putative function
Size aas
581545
MhpC
2-hydroxy-6-ketonona-2,4-dienedioic acid
hydrolase
274
581546/
3337834
MhpD
2-keto-4-pentenoate hydratase
260
581547
oxidoreductase
3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.
1.1 00)
264
581548
MhpF
acetaldehyde dehydrogenase (acetylating; EC 1.2.
1.1 0)
304
581549
MhpE
4-hydroxy-2-oxovalerate aldolase
343
581550
hydratase/decarboxylase
4-oxalocrotonate decarboxylase
262
581551
tautomerase
4-oxalocrotonate tautomerase
63
Overall, several mono- and di-oxygenases were found in the genome, indicating
D. aromatica
has diverse abilities in the aerobic oxidation of heterocyclic compounds.
There are several gene clusters indicative of benzoate transport and catabolism. All
recognized pathways are aerobic. The benzoate dioxygenase cluster BenABCDR is
encoded in VIMSS582483-582487, and is very similar to (and clades with) the xylene
degradation (
xy
/XYZ) cluster of Pseudomonas.
There is also an
hca
A oxygenase gene cluster, embedded in one of the
mhp
clus-
ters (see cluster 5, Figure 1). Specifi city of the large subunit of the dioxygenase
(VIMSS582049) appears to be most likely for a bicyclic aromatic compound, as it
shows highest identity to dibenzothiophene and naphthalene dioxygenases.
Dechloromonas Aromatica's
Sensitivity to the Environment
Cell Signaling
Dechloromonas aromatica
has a large number of genes involved in signaling path-
ways, with 314 predicted signaling proteins categorized in COG T (signal transduction
mechanisms) and a total of 395 proteins (nearly 10% of the genome) either recruited
to COG T or possessing annotated signal transduction domains. Signaling appears to
be an area that has undergone recent gene expansion, as nine recent gene duplication
events in this functional group are predicted by phylogenetic analysis, as described in
a later section (shown in Table 3).
Complex lifestyles are implicated in large genomes with diverse signaling capa-
bility, and in general genomes with a very large number of annotated orfs have high
numbers of predicted signal transducing proteins, as shown in Figure 3, though some
species, such as
Rhodococcus
RHA1 and
Psychrofl exus
torques are notable excep-
tions to this trend. However, assessment of COG T population size relative to other
genomes with a similar number of predicted orfs (Figure 3) indicates that
D. aromatica
is one of a handful of species that have a large relative number of signaling proteins
versus similarly sized genomes. Other organisms displaying this characteristic include
Magnetospirillum magnetotacticum
MS-1,
Stigmatella aurantiaca
,
Myxococcus Xan-
thus
DK1622,
Magnetospirillum magneticum
AMB-1,
Oceanospirillum
sp. MED92,
and
Desulfuromonas acetoxidans
. Within the Betaproteobacteria,
Chromobacterium
