Biology Reference
In-Depth Information
Table 3.
List of genes reannotated during the reconstruction process.
Gene
Old Annotation
New Annotation
Reference
PP0213
5uccinate-semialdehyde dehydrogenase;
EC:1.2.1 .16
Glutarate-semialdehyde; dehydrogenase EC
1.2.1.20
[36]
PP0214
4-Aminobutyrate aminotransferase;
EC:2.6.1.19, EC:2.6.1.22
5-Aminovalerate transaminase; EC 2.6.1.48
[36]
PP0382
Carbon-nitrogen hydrolase family protein
5-Aminopentanamidase; EC 3.5.1.30
[36]
PP0383
Tryptophan 2-monooxygenase, putative
Lysine 2-monooxygenase; EC 1.13.12.2
[36]
PP2336
Aconitate hydratase, putative; EC:4.2.1.3
2-Methylisocitrate dehydratase; EC 4.2.1.99
a
PP2432
Oxygen-insensitive NAD(P)H nitroreduc-
tase; EC:1.-.-.
6,7-Dihydropteridine reductase; EC 1.5.1.34
a
PP3591
Malate dehydrogenase, putative; EC:1.1.1.37 ∆
1
-Piperideine-2-carboxylate reductase; EC
1.5.1.21
[36]
PP4066
Enoyi-CoA hydratase, putative; EC:4.2.1.17
Methylglutaconyi-CoA hydratase; EC
4.2.1.18
[88]
PP4065
3-Methylcrotonyi-CoA carboxylase, beta
subunit, putative
EC:6.4.1.3
Methylcrotonoyi-CoA carboxylase; EC
6.4.1.4
[88]
PP4067
AcCoA carboxylase, biotin carboxylase,
putative; EC:6.4.1 .3
Methylcrotonoyi-CoA carboxylase; EC
6.4.1.4
[88]
PP4223
Diaminobutyrate-2-oxoglutarate transami-
nase; EC:2.6.1.76
Putrescine aminotransferase; EC 2.6.1.82
a
PP4481
Acetylornithine aminotransferase;
EC:2.6.1.11
Succinylornithine transaminase; EC 2.6.1.81
a
PP5029
Formiminoglutamase; EC:3.5.3.8
N-Formylglutamate deformylase; EC 3.5.1.68
a
PP5036
Atrazine chlorohydrolase
N-Formylglutamate deformylase; EC 3.5.1.68
a
PP5257
Oxidoreductase, FAD-binding
L
-Pipecolate oxidase; EC 1.5.3.7
[36]
PP5258
Aldehyde dehydrogenase family protein;
EC:1.2.1.3
L
-Aminoadipate-semialdehyde dehydroge-
nase; EC 1.2.1.31
[36]
a
Analysis of the sequence homology and genomic context information.
Comparison of the Predicted and Measured Growth Yields and the Role of
Maintenance
After completing the reconstruction, we assessed whether the model was capable of
predicting the growth yield of
P. putida
, a basic property of the modeled organism.
In
silico
growth yield on succinate was calculated by FBA and compared with
in vivo
growth yield measured in continuous culture [37]. If the
in silico
yield were lower than
the experimental, it would indicate that the network may lack important reactions that
influence the efficiency of conversion of carbon source into biomass constituents and/
or energy. In fact, the calculated
in silico
yield (0.61 g
DW
⋅
g
C
−1
) was higher than the ex-
perimental yield (0.47 g
DW
⋅
g
C−1
), indicating that some of the processes reconstructed
in the network might be unrealistically efficient and/or that
P. putida
may be diverting
resources into other processes not accounted for in the model. This greater efficiency
of the
in silico
model versus
in vivo
growth data is also consistent with recent studies
that suggest optimal growth is not necessarily the sole objective (function) of bio-
chemical networks [38, 39].
