Biology Reference
In-Depth Information
violaceum
, and
Thiobacillus denitrifi cans
have a relatively large number of signaling
cascade genes, but still have far fewer than found in
D. aromatica
, with 262 predicted
COG T proteins (6% of the genome) and 137 COG T proteins (4.8% of the genome),
respectively. Histidine kinase encoding proteins are particularly well-represented,
with only
Stigmatella aurantiaca
DW4/3-1,
Magnetococcus
sp. MC-1,
Myxococcus
xanthus
DK1622, and
Nostoc punctiforme
reported as having more. The 68 anno-
tated histidine kinases include a large number of nitrate/nitrogen responsive elements.
Furthermore, the presence of 47 putative histidine kinases predicted to contain two
transmembrane (TM) domains, likely to encode membrane-bound sensors (see Figure
4), suggests that
D. aromatica
is likely to be highly sensitive to environmental signals.
Nearly half (48%) of the predicted histidine kinases are contiguous to a putative re-
sponse regulator on the chromosomal DNA, indicating they likely constitute function-
ally expressed kinase/response regulator pairs. This is atypically high for contiguous
placement on the chromosome [39].
Table 3.
Candidates for gene expansion in the
D. aromatica
genome.
Protein/protein family function
Number of duplicates
Number of triplicates
Transport (membrane)
12
Signal transduction or regulatory- includes:
9
FlhD homolog
(1)
FlhC homolog
(1)
Nitrogen regulatory protein Pll homolog
(1)
Hydrolase/transhydrogenase or hydratase
4
1
Cytochromes
3
2
Mhp family
2
2
Phospholipase/phosphohydrolase
2
1
Phasin
1
Dioxygenase
1
NapH homolog
1
NosZ homolog
1
Unknown function
7
A relatively high level of diguanylate cyclase (GGDEF domain [40-42]) signal-
ing capability is implied in
D. aromatica
by the presence of 57 proteins encoding a
GGDEF domain (Interpro IPR000160) and an additional 10 with a GGDEF response
regulator (COG1639) [40]. The
E. coli
, for comparison, encodes 19. This gene family
also appears to have undergone recent expansion in this microbe's evolutionary his-
tory. Microbes having a large number of proteins or even a diverse array of COG T
elements do not a priori encode a large number of GGDEF elements, as
Stigmatella
aurantiaca
,
Myxococcus
,
Xanthus
DK1622, and
Burkholderia pseudomallei
, by con-
trast, have very large genomes with extensive COG T populations, yet each have 20 or
fewer proteins identifi ed as having GGDEF domains, and
Prochloroccus
spp. appear
to have none. Conversely,
Oceanospirillum
has a relatively small genome, yet has 112
proteins identifi ed as likely GGDEF domain/IPR000160 proteins. The GGDEF/EAL
