Appendix
1 A1 Overall comparison of iSS884 & iBB814
Specification
iSS884
iBB814
Semi-Automatic
1332
Manual
1371
Cytosol
824
757
Mitochondria
207
125
Peroxisome
60
N/A
Transport
239
489
Metabolites
922
644
Genes
884
814
15.1
14.4
Cytosol, Exchange,
Mitochondria, Peroxisome
Cytosol, Exchange
Mitochondria
Approach
Reactions
Percent of Genome (%)
Compartment
2 A2 Model comparison under aerobic condition
through the SID framework
(a)
(b)
Figure S2: The SID framework identifies how fluxes are affected by the increased oxygen
uptake rate under aerobic condition in model iSS884 (a) and iBB814 (b).
Color code: red – flux decrease, green – flux increase, gray – not affected. Line width indicates
effect level.
3 A3 Fatty Acid Biosynthesis
For iSS884, the synthesis of saturated fatty acid is carried out by a series of combination
reactions, each of which increases the length of the fatty acid chain by 2 as shown in Figure S2,
where two examples are given: (a) the formation of butyryl-[ACP] (4 carbons) from acetyl-CoA
(2 carbons), and (b) the formation of ocetadecanoyl-[ACP] and octadecanoic acid (both with 18
carbons) from hexadecanoyl-[ACP] (with 16 carbons). There are totally 8 synthesis reactions in
iSS884 to form ACP bounded fatty acids with length 4 up to 18, and they exist in both cytosol
and mitochondria. However, there are only 4 hydrolysis reactions that remove the ACP group to
form fatty acids (as shown in the box in Figure S2 (b)) for carbon length 12 up to 18. This means
that the saturated fatty acids with carbon chain length less than 12 are not available (as they are
all ACP bounded) in the cell.
2
4
2
(a)
16
18
(b)
Figure S3 Fatty acid biosynthesis for iSS884: (a) formation of butyryl-[ACP], and (b) formation
of ocetadecanoyl-[ACP] and octadecanoic acid.
In contrast, iBB814 can form a variety of saturated, unsaturated, and odd chain length fatty acids.
For example, Figure S3 (a) shows how decanoate (10 carbons) is produced from octanoate (8
carbons). At the same time, a similar reaction exists, as shown in Figure S3 (b), to produce
decanoyl-CoA from octanoyl-CoA. Reactions similar to these two exist in cytosol to synthesize
fatty acids with length from 4 up to 26. Note that the reactions in iBB814 are somewhat
simplified, as they skip all the intermediate steps (and the intermediate metabolites) that involved
in iSS884. In addition, all synthesis reactions in iBB814 have the hydrolysis step, therefore no
ACP bounded fatty acids are produced in cytosol. Instead, ACP bounded fatty acids are produced
in the mitochondria only. One example is shown in Figure S3 (c), where decanoyl-[ACP] is
produced from octanoyl-[ACP]. The ACP bounded fatty acids are then transported to cytosol,
where the ACP group is removed through hydrolysis, as shown in Figure S3 (d).
2
8
10
(a)
(b)
(c)
12
12
(d)
Figure S3 Examples of fatty acid biosynthesis for iBB814: (a) fatty acid, (b) fatty acid bonded
with CoA, (c) fatty acid bonded with ACP (d) Hydrolysis of ACP group
4 A4 Biomass Composition
4.1 Amino acids
Amino Acid
iSS884
iBB814
ala-L[c]
0.496
0.4735
arg-L[c]
0.1783
0.1821
asn-L[c]
0.0719
0.1511
asp-L[c]
0.100
0.1566
cys-L[c]
0.0415
0.0511
gln-L[c]
0.447
0.1817
glu-L[c]
0.447
0.3190
gly[c]
0.186
0.4724
his-L[c]
0.143
0.1005
ile-L[c]
0.138
0.1454
leu-L[c]
0.0799
0.251
Amino Acid
lys-L[c]
met-L[c]
L-orn[c]
phe-L[c]
pro-L[c]
ser-L[c]
thr-L[c]
trp-L[c]
tyr-L[c]
val-L[c]
4.2 Carbohydrates
Carbohydrates
iSS884
13BDglcn[c]
1.798
chitin[c]
Not Present
glycogen[c]
0.178
mannan[c]
Not Present
tre[c]
0.0102
Fatty Acids
clpn[c]
eig3p[c]
ergst[c]
fecost[c]
hdca[c]
lanost[c]
ocdca[c]
pa[c]
pc[c]
4.3 Fatty Acids
iSS884
iBB814
0.002
Not Present
0.0007
Not Present
0.0388
0.0560
0.0007
Not Present
0.0119
Not Present
0.0002
Not Present
0.0029
Not Present
0.001
Not Present
2.55 x 10-3
iSS884
0.200
0.1577
0.0258
0.0315
0.141
0.1359
0.128
0.0483
0.033
0.166
iBB814
0.2624
0.0559
Not Present
0.1147
0.1592
0.2330
0.1809
0.0248
0.0741
0.2201
iBB814
0.6107
0.4528
0.2714
0.7156
0.076
Fatty Acids
pe[c]
ps[c]
ptd1ino[c]
9ZHexdece[c]
9ZOctadece[c]
9Z12ZOctadecad[c]
(9Z,12Z,15Z)Ocdeat[c]
(9Z,12Z,15Z)Ocdeat[c]
zymst[c]
iSS884
0.064
0.001
0.003
0.0043
0.0199
0.0218
0.0179
iBB814
4.1 x 10-5
Not Present
1.5 x 10-5
Not Present
Not Present
Not Present
Not Present
0.0179
Not Present
0.002
Not Present
Nucleotides
atp[c]
amp[c]
cmp[c]
gmp[c]
ump[c]
damp[c]
dcmp[c]
dgmp[c]
dtmp[c]
4.4 Nucleotides
iSS884
iBB814
39.92
44.4
0.078
0.0444
0.0545
0.0388
0.05469
0.0361
0.0781
0.0522
0.009
0.0112
0.0063
0.0084
0.0063
0.0084
0.009
Not Present
4.5 Other metabolites
Other
iSS884
h2o[c]
39.92
adp[c] (right hand side)
39.92
pi[c] (right hand side)
39.92
h[c] (right hand side)
39.92
iBB814
44.4
44.4
44.4
44.4