Biology Reference
In-Depth Information
Table 2.
Summary of the comparison with the BIOLOG substrate utilization assay.
Compounds tested
95
Utilized compounds
47
Reconstruction version
iJP815
Pre2
iJP815
Tested compounds included in 47 51 the model
47
51
Utilized compounds included in the model
33
37
Compound supply
Ext
lnt
Ext
lnt
True positives
14
28
23
33
True negatives
48 (14)
42 (8)
48 (14)
42 (8)
False positives
0
6
0
6
False negatives
33 (19)
20 (6)
24 (14)
14 (4)
Values in brackets indicate onl those compounds that iJP815 accounts for.
The initial working version of the model (iJP815
pre2
) was able to simulate growth
with 14 of the 47 BIOLOG-assayed compounds as sole carbon sources. This version
of the reconstruction contained only a few transport reactions, prompting us to identify
compounds that could not be utilized
in silico
simply due to the lack of a transporter.
This was achieved by allowing the intracellular pool of each compound of interest to
be exchanged with environment
in silico
, and by evaluating the production of bio-
mass in each case through FBA simulations. This approach increased the number of
utilizable substances to 34 but also produced six false positives (i.e., substances that
support
in silico
growth, but which gave a negative phenotype in the BIOLOG assay).
These included three metabolites involved in central metabolic pathways (D-glucose
1-phosphate, D-glucose 6-phosphate and glycerol-3-phosphate), an intermediate of
the L-histidine metabolism pathway (urocanate), an intermediate of branched amino
acids biosynthesis (2-oxobutanoate), and the storage compound glycogen. This analy-
sis suggests that the inability of
P. putida
to utilize these compounds
in vivo
is likely
due to the lack of appropriate transport machinery.
The fi nal
P. putida
model (iJP815) grew on 39 of the 51 compounds tested in the
BIOLOG assay and that concurrently were accounted for in the model. Of these, 33
were true positives (compounds utilized
in vivo
and allowing for growth
in silico
). The
mode of utilization of the remaining 14
in vivo
oxidized compounds (i.e., false nega-
tives) could not be elucidated. The remaining 42 compounds posed true negatives,
eight of which were accounted for in the reconstruction. Ten utilized compounds also
lack transport reactions, as nothing is known about their translocation into the cell.
Nevertheless, this comparison of
in silico
growth predictions with BIOLOG substrate
utilization data indicates that the core metabolism of
P. putida
has been properly re-
constructed.
A note of caution when comparing the BIOLOG assays with growth predictions is
that this assay evaluates whether an organism is able to oxidize the tested compound
and yield energy from it, which is different from growth. However, as
P. putida
is able
