Biology Reference
In-Depth Information
Figure 5.
Sulfur oxidation (thiosulfate to sulfate) candidates in
R. eutropha
,
R. palustris
, and
D.
aromatica
. Proposed model for this periplasmic complex is as follows: SoxXA, oxidatively links
thiosulfate to SoxY; SoxB, potential sulfate thiohydrolase, interacts with SoxYZ (hydrolyzes sulfate
from SoxY to regenerate); SoxCD, a sulfur dehydrogenase; oxidizes persulfide on SoxY to cysteine-
S-sulfate and potentially yields six electrons per sulfate; SoxC, sulfite oxidase/dehydrogenase with
homology to nitrate reductase, induced by thiosulfate; SoxDE, both c-type cytochromes with two
heme-type binding sites; and SoxF, a FAD flavoprotein with sulfide dehydrogenase activity. Cyt,
cytochrome.
Conversely, the cytoplasmic SorAB complex [96] is not present in
D. aromatica
nor
A. aromaticum
EbN1, although it is found in several other Betaproteobacteria,
including
R. metallidurans
,
R. eutropha
,
R. solanacearum
,
C. violaceum
, and
B.
japonicum
.
Gene Family Expansion
To determine candidates for recent gene duplication events, extensive phylogenomic
profile analyses were conducted for all sets of paralogs in the genome. Flower Power
recruitment and clustering against the non-redundant Genbank protein set was done,
and the resulting alignments were analyzed using the tree-building SCI-PHY or Belvu
based neighbor-joining utilities. The alignment of two or more
D. aromatica
protein
sequences in a clade such that they displayed higher % identity to each other than to
orthologs present in other species was interpreted as an indication of a probable recent
duplication event, either in the
D. aromatica
genome itself or in a progenitor species.
Results of this analysis are shown in Table 3.
