Biology Reference
In-Depth Information
general
Azoarcus
BH72 appears to share many families of proteins with
D. aromatica
that are not present in
A. aromaticum
EbN1 (e.g., signaling proteins, noted below).
Anaerobic degradation of benzene occurs at relatively sluggish reaction rates, in-
dicating that the pathways incumbent in
D. aromatica
for aromatic degradation under
anaerobic conditions might serve in a detoxifi cation role. Another intriguing possibil-
ity is that oxidation is dependent on intracellularly produced oxygen, which is likely
to be a rate-limiting step.
Alicycliphilus denitrifi cans
strain BC couples benzene deg-
radation under anoxic conditions with chlorate reduction, utilizing the oxygen pro-
duced by chlorite dismutase in conjunction with a monooxygenase and subsequent
catechol degradation for benzene catabolism [26]. A similar mechanism may account
for anaerobic benzene oxidation coupled to perchlorate and chlorate reduction in
D.
aromatica
. However, anaerobic benzene degradation coupled with nitrate reduction is
also utilized by this organism, and remains enigmatic [5].
The extremely high divergence of encoded protein families in this functional
grouping differs from the general population of central metabolic and housekeeping
genes:
Azoarcus
BH72,
Azoarcus aromaticum
EbN1 and
D. aromatica
are evolution-
arily near-neighbors within currently sequenced genomes, as defi ned both by the high
level of protein similarity within housekeeping genes (defi ned by the COG J family of
proteins), and 16sRNA sequence.
Azoarcus
BH72 and
A. aromaticum
EbN1 display
the highest percent similarity between housekeeping proteins within this triad, with
138 of the 156 COG J proteins in
A. aromaticum
EbN1 displaying highest similarity
to their BH72 counterparts. On average these two genomes display 83.5% amino acid
identity across shared COG J proteins.
Dechloromonas aromatica
is an outlier in the
triad, with higher similarity to
Azoarcus
BH72 than
A. aromaticum
EbN1 (43 of
D.
aromatica's
169 COG J proteins are most homologous to
A. aromaticum
EbN1 ortho-
logs with an average 71% identity, and 67 are most homologous to
Azoarcus
BH72
with an average 72% identity).
Comparative genomics have previously established that large amounts of DNA
present in one species can be absent even from a different strain within the same spe-
cies [27]. In addition, the underestimation of the diversity of aromatic catabolic path-
ways (both aerobic and anaerobic) has been noted previously [28], and a high level of
enzymatic diversity has been seen for pathways that have the same starting and end
products, including anaerobic benzoate oxidation [29].
Aerobic Aromatic Degradation
Dechloromonas
aromatica
encodes several aerobic pathways for aromatic degrada-
tion, including six groups of oxygenase clusters that each share a high degree of se-
quence similarity to the phenylpropionate and phenol degradation (HPP and
Mhp
)
pathways in
Comamonas
species [30, 31]. The
mhp
genes of
E. coli
and
Comamonas
are involved in catechol and protocatechuate pathways for aromatic degradation via
hydroxylation, oxidation, and subsequent ring cleavage of the dioxygenated species.
Only one of the clusters in
D. aromatica
encodes an
mhp
A-like gene; it begins with
VIMSS584143
Mhp
C, and is composed of orthologs of MhpABCDEF&R, and is in
the same overall order and orientation as the
Comamonas
cluster as well as the
E. coli
