Download Candida tropicalis biomass composition calculation

Supplementary 1: Biomass composition and energy
requirements of Candida tropicalis
Table of Contents
Candida tropicalis biomass composition calculation ............................... 1
Overall cellular composition .................................................................................................. 1
Amino acid composition ........................................................................................................ 2
Carbohydrates composition (Brondz and Olsen 1990) .......................................................... 3
DNA composition ................................................................................................................... 3
RNA composition (Dujon et al. 2004) .................................................................................... 4
Lipid composition ................................................................................................................... 4
Growth associated ATP requirement for polymerization ...................................................... 6
Additional biomass components (Xu et al. 2013) .................................................................. 6
Biomass composition summary ............................................................................................. 7
Non-growth associated ATP maintenance (NGAM) requirement ............8
Candida tropicalis biomass composition calculation
In the following calculations, general information such as molecular weight (MW) and
chemical formula of each compound are obtain from the online PubChem database.
Overall cellular composition
Component
Cellular content (g/gDCW)
Reference
Protein
0.5300
Batch cultivations in minimal medium
RNA
0.0630
(Verduyn et al.
Referring to
1990)
S.cerevisiae
(Verduyn et al.
Referring to
1990)
S.cerevisiae
(Goyal and
Referring to C.albicans
DNA
Lipid
0.0040
0.0395
Remark
Khuller 1992)
Carbohydrate
s
0.4000
(Brondz and
Referring to T.glabrata
Olsen 1990)
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Amino acid composition
The composition of aspartate cannot be distinguished from that of asparagine and this is
also the same for glutamine and glutamate. Thus, we assume equal distribution of the
composition within the pairs of amino acids. The molecular weight of the amino acids given
in the following table excludes the weight of the water molecule that was lost during the
formation of peptide bonds.
Amino acid
Content(mg/gDCW) MW-H2O(g/mol)
mmol/gDCW
Aspartate
3.8690
114.11
0.0339
Glutamate
42.5590
128.13
0.3321
Serine
26.4470
87.09
0.3037
Histidine
20.1400
137.16
0.1468
Glycine
22.9490
57.07
0.4021
Threonine
23.7970
101.12
0.2353
Arginine
0.0820
157.21
0.0005
Alanine
37.8950
71.09
0.5330
Tyrosine
29.5740
163.19
0.1812
Cysteine
5.1940
103.16
0.0503
Valine
37.7360
99.15
0.3806
Methionine
45.6330
131.21
0.3478
Phenylalanine
30.3690
147.19
0.2063
Isoleucine
22.5780
113.18
0.1995
Leucine
41.9760
113.18
0.3709
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Lysine
68.7410
129.20
0.5321
Proline
20.2990
97.13
0.2090
Glutamine
42.5590
129.13
0.3296
Asparagine
3.8690
114.12
0.0339
Tryptophan
14.4720
186.23
0.0777
Carbohydrates composition (Brondz and Olsen 1990)
The total content of carbohydrate was equal to the contents of glucan 1,3 in the biomass
function. .
Component
Content(w/w)
MW-H2O
mmol/gDCW
(g/mol)
Mannose
0.2770
162
0.6839
Glucose
0.5180
162
1.2790
Galactose
0.2050
162
0.5061
DNA composition
GC content of Candida tropicalis is about 33.2% (Butler et al. 2009).
Nucleotide
DNA (mol/mol)
MW-ppi (g/mol)
DNA (mmol/gDCW)
dATP
0.3350
312.202
0.0043
dCTP
0.1650
286.16
0.0023
dGTP
0.1650
328.201
0.0020
dTTP
0.3350
303.187
0.0044
Page | 3
RNA composition (Dujon et al. 2004)
RNA composition of C. tropicalis, referring to C. glabrata
Nucleotide
RNA (mol/mol)
MW-ppi (g/mol)
RNA
(mmol/gDCW)
mRNA(5%)
tRNA(75%)
rRNA(20%)
ATP
0.3350
0.2950
0.3685
328.20
0.0696
CTP
0.1650
0.2050
0.1164
304.18
0.0273
GTP
0.1650
0.2050
0.0830
344.20
0.0224
UTP
0.3350
0.2950
0.4321
305.16
0.0791
Lipid composition
The composition of lipids were calculated from data obtained from (Dey and Maiti 2013).
Before we can evaluate the composition of lipids, we need to calculate the average
molecular weight of a fatty acid chain based on data reported by Dey and Maiti:
Fatty acid
(w/w %)
Content(w/w) MW(g/mol)
mmol/g FA
mol % FA
C120
4.6
0.046
200.32
0.23
0.0619
C160
24.6
0.246
255.40
0.96
0.2596
C161
3.8
0.038
253.40
0.15
0.0404
C170
1.4
0.014
270.45
0.05
0.0140
C180
50.2
0.502
283.50
1.77
0.4773
C181
15.4
0.154
281.50
0.55
0.1475
Page | 4
Taking the inverse of the sum of the values in the “mmol/g FA” column gives us the average
molecular weight of a fatty acid chain to be 269.54 g/mol. Using the data by (Goyal and
Khuller 1992), we can evaluate the molecular weights and composition of the phospholipids
by adding the weight of the respective number of fatty acid chains to the phosphatecontaining core structure of the phospholipids. We have used the relative abundance of
different phospholipids as reported by Goyal and khuller. By taking into consideration that
the total cellular lipid composition is 0.0395 g/gDCW, we can calculate the individual lipid
composition:
Phospholipid Content(g/g
Core
phospholipid) MW
No. of
Lipid
mmol/g
mmol/gDCW
FA
MW(g/mol)
phosholipid
PC
0.2014
312.230 2
851.31
0.23657657
0.0009
PE
0.1358
269.150 2
808.23
0.168021479 0.0006
PI
0.1208
388.220 2
927.3
0.130270678 0.0005
PS
0.1656
383.290 2
922.37
0.179537496 0.0007
PA
0.0360
226.080 2
765.16
0.047076326 0.0002
Sterol composition data given for C.albicans by (Ghannoum, Swairjo, and Soll 1990) is
converted to biomass composition using the values of 0.0395 g lipid/gDCW given by Goyal
and Khuller..
Component
Content(w/w lipid)
MW(g/mol)
mmol/g lipid
mmol/gDCW
Lanosterol
0.1050
426.3862
0.2463
0.00136
Page | 5
Squalene
0.0280
410.3913
0.0682
0.00038
Ergosterol
0.7600
396.3392
1.9175
0.01060
Growth associated ATP requirement for polymerization
The ATP requirement for polymerization of each species is obtained from (Verduyn, 1991).
Polymer
g/gDCW
mmol ATP/g polymer
mmol ATP/gDCW
Protein
0.53
37.7
19.981
Carbohydrate
0.4
12.8
5.12
RNA
0.063
26
1.638
DNA
0.004
26
0.104
Total growth associated ATP requirement is 26.843 mmol ATP/gDCW.
Additional biomass components (Xu et al. 2013)
We include some essential metabolites in the biomass composition so as to qualitative
account for the essentiality of their synthesis pathways. The composition of these
metabolites is summarized in the following table:
Molecule
MW (g/mol)
w/w soluble
mmol / gDCW
pool
FAD
783.54
0.1000
0.0012
Thiamine(1+) diphosphate 422.30
0.1000
0.0022
NAD
662.42
0.1000
0.0014
NADP
740.39
0.1000
0.0012
COA
763.51
0.1000
0.0012
Page | 6
FMN
456.00
0.1000
0.0020
5-Methyltetrahydrofolate
458.46
0.1000
0.0020
Biomass composition summary
Metabolite
mmol/gDCW
Metabolite
mmol/gDCW
Aspartate
0.0339
FAD
0.0012
Glutamate
0.3321
Thiamine(1+) diphosphate
0.0022
Serine
0.3037
NAD
0.0014
Histidine
0.1468
NADP
0.0012
Glycine
0.4021
COA
0.0012
Threonine
0.2353
FMN
0.0020
Arginine
0.0005
5-Methyltetrahydrofolate
0.0020
Alanine
0.5330
dATP
0.0043
Tyrosine
0.1812
dCTP
0.0023
Cysteine
0.0503
dGTP
0.0020
Valine
0.3806
dTTP
0.0044
Methionine
0.3478
CTP
0.0273
Phenylalanine
0.2063
GTP
0.0224
Isoleucine
0.1995
UTP
0.0791
Leucine
0.3709
Lanosterol
0.00136
Lysine
0.5321
Squalene
0.00038
Proline
0.2090
Ergosterol
0.01060
Glutamine
0.3296
PC
0.0009
Page | 7
Asparagine
0.0339
PE
0.0006
Tryptophan
0.0777
PI
0.0005
13BDglcn
2.46
PS
0.0007
triglyc
0.02
PA
0.0002
Non-growth associated ATP maintenance (NGAM) requirement
The NGAM refers to the amount of ATP required by the cell even when it is not growing.
This energy consumed for purposes other than the production of new cell material has been
extensively reviewed (Van Bodegom 2007). In this study, we determined the NGAM
requirement for our chemostat experiment using a conventional method of finding the yintercept of the plot of glucose uptake rate against dilution rate (Pirt 1982).
By maximizing ATP turnover under the glucose uptake constraint of 1 mmol/gDCW-hr, the
ATP yield is evaluated as YATP, max = 17 mol ATP/ mol glucose. Using this value and the yintercept (0.2292 mmol glucose/gDCW-hr), we can calculate the NGAM requirement to be
about 3.8964 mmol ATP/gDCW-hr.
Page | 8
References
Van Bodegom, Peter. 2007. “Microbial Maintenance: A Critical Review on Its
Quantification.” Microbial Ecology 53: 513–23.
Brondz, I., and I. Olsen. 1990. “Multivariate Analyses of Cellular Carbohydrates and Fatty
Acids of Candida Albicans, Torulopsis Glabrata, and Saccharomyces Cerevisiae.” Journal
of Clinical Microbiology 28: 1854–57.
Butler, Geraldine et al. 2009. “Evolution of Pathogenicity and Sexual Reproduction in Eight
Candida Genomes.” Nature 459: 657–62.
Dey, P., and M. K. Maiti. 2013. “Molecular Characterization of a Novel Isolate of Candida
Tropicalis for Enhanced Lipid Production.” Journal of Applied Microbiology 114: 1357–
68.
Dujon, Bernard et al. 2004. “Genome Evolution in Yeasts.” Nature 430: 35–44.
Ghannoum, M A, I Swairjo, and D R Soll. 1990. “Variation in Lipid and Sterol Contents in
Candida Albicans White and Opaque Phenotypes.” Journal of medical and veterinary
mycology : bi-monthly publication of the International Society for Human and Animal
Mycology 28: 103–15.
Goyal, S, and G K Khuller. 1992. “Phospholipid Composition and Subcellular Distribution in
Yeast and Mycelial Forms of Candida Albicans.” Journal of medical and veterinary
mycology : bi-monthly publication of the International Society for Human and Animal
Mycology 30: 355–62.
Pirt, S J. 1982. “Maintenance Energy: A General Model for Energy-Limited and EnergySufficient Growth.” Archives of microbiology 133: 300–302.
Verduyn, C, E Postma, W a Scheffers, and J P van Dijken. 1990. “Physiology of
Saccharomyces Cerevisiae in Anaerobic Glucose-Limited Chemostat Cultures.” Journal
of general microbiology 136: 395–403.
Xu, Nan et al. 2013. “Reconstruction and Analysis of the Genome-Scale Metabolic Network
of Candida Glabrata.” Molecular bioSystems 9(2): 205–16.
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