Biology Reference
In-Depth Information
Metabolic Cycles
Nitrogen
Dechloromonas aromatica
closely reflects several metabolic pathways of
R. capsula-
tus
, which is present in the rhizosphere, and its assimilatory nitrate/nitrite reductase
cluster is highly similar to the
R. capsulatus
cluster [72]. Encoded nitrate response
elements also indicate a possible plant association for this microbe, as nitrate can act
as a terminal electron acceptor in the oxygen-limited rhizosphere. Alternatively, NO
reduction can indicate the ability to respond to anti-microbial NO production by a host
(used by the host to mitigate infection [73]). Several gene families are present that
indicate interactions with a eukaryotic host species, including response elements that
potentially neutralize host defense molecules, in particular nitric oxide (NO) and other
nitrogenous species.
Nitrate is imported into the cytosol by NasDEF in
Klebsiella pneumoniae
[74]
and expression of nitrate and nitrite reductases is regulated by the nasT protein in
Azotobacter vinelandii
[75]. A homologous set of these genes are encoded by the
cluster VIMSS580377-580380 (NasDEFT), and a homolog of
nar
K is immediately
downstream at VIMSS580384, and is likely involved in nitrite extrusion. Upstream,
a putative nasA/nirBDC cluster (assimilatory nitrate and nitrite reduction) is encoded
near the
nar
XL-like nitrate response element. The VIMSS580393 encodes a nitrate
reductase that is homologous to the NasA cytosolic nitrate reductase of
Klebsiella
pneumoniae
[76]. Community studies have correlated the presence of NasA-encoding
bacteria with the ability to use nitrate as the sole source of nitrogen [77]. The large
and small subunits of nitrite reductase (VIMSS580391 nirB and VIMSS580390 nirD)
are immediately adjacent to a transporter with a putative nitrite transport function
(VIMSS580389 NirC-like protein). The NirB orf is also highly homologous to both
NasB (nitrite reductase) and NasC (NADH reductase which passes electrons to NasA)
of
Klebsiella pneumoniae
. The HMMs created from alignments seeded by the NasB
and NasC genes scored at 3.2e
-193
and 4.0e
-159
, respectively, to the VIMSS580391 NirB
protein.
Dechloromonas aromatica
is similar to
Methylococcus capsulatus
,
Ralstonia
solanacearum
,
Polaromonas
, and
Rhodoferax ferrireducens
for
nas
A,
nir
B, and
nir
D
gene clusters. However, the presence of the putative transporter
nir
C (VIMSS580389)
shares unique similarity to the
E. coli
and
Salmonella nir
BCD clusters.
Putative periplasmic, dissimilatory nitrate reduction, which is a candi-
date for denitrifi cation capability [78], is encoded by the
nap
DABC genes
(VIMSS3337807/581796-581799). A probable cytochrome c', implicated in NO bind-
ing as protection against potentially toxic excess NO generated during nitrite reduc-
tion [79], is encoded by VIMSS582015. Although most denitrifi ers are free living,
plant-associated denitrifi ers do exist [80]. There is no dissimilatory nitrate reductive
complex
nar
GHIJ, but rather,
Nar
G and
Nar
H-like proteins are found in the evolu-
tionarily-related perchlorate reductase alpha and beta subunits [24]. These proteins
are present in the pcrABCDcld cluster, VIMSS582649-582652 and VIMSS584327, as
previously reported for
Dechloromonas
species [81].
Ammonia incorporation appears to be metabolically feasible via a putative glu-
ammonia ligase (VIMSS581081), an enzyme that incorporates free ammonia into the
