Biology Reference
In-Depth Information
(
Helicobacter pylori
and
Campylobacter jejuni
), and displays eukaryotic host interac-
tions, yet is not known to be pathogenic [85]. The distinction between effector mol-
ecules causing a pathogenic interaction and a symbiotic one is unclear.
Nitrogen Fixation
Nitrogen fixation capability in
D. aromatica
is indicated by a complex of
nif
-like
genes (see Table 4), that include putative nitrogenase alpha (NifD, VIMSS583693)
and beta (NifK, VIMSS583694) subunits of the molybdenum-iron protein, an ATP-
binding iron-sulfur protein (NifH, VIMSS583692), and the regulatory protein NifL
(VIMSS583623), that share significant sequence similarity and synteny to the free-
living soil microbe
Azotobacter vinelandii
.
Dechloromonas
aromatica
further en-
codes a complex that is likely to transport electrons to the nitrogenase, by using a
six subunit rnfABCDGE-like cluster (VIMSS583616-583619, 583621, and 583622)
that is phylogenomically related to the
Rhodobacter capsulatus
complex used for
nitrogen fixation [86]. There is a second
rnf
-like NADH oxidoreductase complex
composed of VIMSS583911-583916, of unknown involvement (see Figure 4).
Aromatoleum aromaticum
EbN1 and
Azoarcus
BH72 each encode two
rnf
-like clus-
ters as well.
Embedded in the putative nitrogen fi xation cluster are two gene families involved
in urea metabolism (Table 4). This includes the urea transport proteins (UrtABCDE)
and urea hydrolase enzyme family (Ure protein family).
Hydrogenases Associated with Nitrogen Fixation
Uptake hydrogenase is involved in the nitrogen fixation cycle in root nodule
symbionts where it is thought to increase efficiency via oxidation of the co-
produced hydrogen (H2) [87].
Dechloromonas
aromatica
encodes a cluster of
13 predicted orfs (Hydrogenase-1 cluster, VIMSS581358-581370; Table 5) that
includes a hydrogenase cluster syntenic to the
hox
KGZMLOQR(T)V genes
found in
Azotobacter vinelandii
, which reversibly oxidize H
2
in that organism
[88]. This cluster is followed by a second hydrogenase (Hydrogenase-2 cluster,
VIMSS581373-581383). The hydrogenase assembly proteins,
hyp
ABF and CDE
are included (VIMSS581368-581370 and 581380-581381, and VIMSS3337851
(formerly 581382)) as well as proteins related to the hydrogen uptake (
hup
) genes
of various rhizobial microbes [87]. The second region, with the
hyp
and
hyd
-like
clusters, lacks overall synteny to any one genome currently sequenced. It does,
however, display regions of genes that share synteny with
Rhodoferax ferrireducens
,
which displays the highest percent identity across the cluster, both in terms of
synteny and protein identity.
The VIMSS581384 encodes a homolog of the HoxA hydrogenase transcriptional
regulator, which has been shown to be expressed only during symbiosis in some spe-
cies [89]. Regulation is indicated by homologs of NtrX (VIMSS581123) and NtrY
(VIMSS581124); the NtrXY pathway comprises a two-component signaling system
involved in the regulation of nitrogen fi xation in
Azorhizobium caulinodans
ORS571
[90].
