Biology Reference
In-Depth Information
cbbM
type II isoform of RuBisCo [92]; this sub-type is shared by a only a few micro-
bial species.
Further putative Cbb proteins are encoded by VIMSS581680 and 581688, candi-
dates for CbbR (regulator for the cbb operon) and CbbY (found downstream of RuBisCo
in
R. sphaeroides
[93]), respectively.
The presence of the
cbbM
gene suggests the ability to carry out the energetically
costly fi xation of CO
2
, though such functionality has yet to be observed, and CO
2
fi xa-
tion capability has been found in only a few members of the microbial community.
There is a potential glycolate salvage pathway indicated by the presence of two
isoforms of phosphoglycolate phosphatase (
gph
, VIMSS583850 and 581830). In other
organisms, phosphoglycolate results from the oxidase activity of RuBisCo in the Calvin
cycle, when concentrations of CO
2
are low relative to oxygen. In
Ralstonia
(
Alcaligenes
)
eutropha
and
Rhodobacter sphaeroides
, the gph gene (
cbbZ
) is located on an operon
along with other Calvin cycle enzymes, including RuBisCo. In
D. aromatica
, the
gph
candidates for this gene (VIMSS583850 and 581830), are removed from the other
cbb
genes on the chromosome in
D. aromatica
; however VIMSS581830 is adjacent to a
homolog of Ribulose-phosphate 3-epimerase (VIMSS581829,
rpe
).
The
cco
SNOQP gene cluster codes for a cbb-type cytochrome oxidase that func-
tions as the terminal electron donor to O
2
in the aerobic respiration of
Rhodobacter
capsulatus
[94]. These genes are present in a cluster as VIMSS580484-580486 and
VIMSS584273-584274; note that these genes are present in a large number of Beta-
proteobacteria.
Other carbon cycles, such at the reverse TCA cycle and the Wood-Ljungdahl path-
ways, are missing critical enzymes in this genome, and are not present as such.
Sulfur
Sulfate and thiosulfate transport appear to be encoded in the gene cluster composed of
an OmpA type protein (VIMSS581631) followed by orthologs of a sulfate/thiosulfate
specific binding protein Sbp (VIMSS581632), a CysU or T sulfate/thiosulfate trans-
port system permease T protein (VIMSS581633), a CysW ABC-type sulfate transport
system permease component (VIMSS581634), and a CysA ATP-binding component
of sulfate permease (VIMSS581635).
In addition, candidates for the transcriptional regulator of sulfur assimilation from
sulfate are present and include: CysB, CysH, and CysI (VIMSS582364, 582360, and
582362, respectively).
A probable sulfur oxidation enzyme cluster is present and contains homologs of
SoxFRCDYZAXB
[95], with a putative SoxCD sulfur dehydrogenase, SoxF sulfi de de-
hydrogenase, and SoxB sulfate thiohydrolase, which is predicted to support thiosulfate
oxidation to sulfate (see Figure 5). Functional predictions are taken from Friedrich et
al. [95]. A syntenic
sox
gene cluster is also found in
Anaeromyxobacter dehalogens
(although it lacks soxFR) and
Ralstonia eutropha
, but not in
A. aromaticum
EbN1.
Thiosulfate oxidation, however, has not been reported under laboratory conditions
tested thus far, and experimental support for this physiological capability awaits fur-
ther investigation.
