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Infection related stress adaptations in the secretome and wall proteome ofCandida albicans
Sorgo, A.G.
Publication date2013
Link to publication
Citation for published version (APA):Sorgo, A. G. (2013). Infection related stress adaptations in the secretome and wall proteomeof Candida albicans.
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Download date:25 May 2021
Chapter 2
Mass spectrometric analysis of the secretome ofCandida albicans
Yeast (Chichester, England)
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The pathogenic fungus Candida albicans secretes a considerable number of
hydrolases and other proteins. In-depth studies of the C. albicans secretome
could thus provide new candidates for diagnostic markers and vaccine
development. We compared various growth conditions differing in pH,
temperature, and the presence of the hyphal inducer N-acetylglucosamine. The
polypeptide content of the growth media was ca. 0.1 - 0.2% of the total biomass.
Using LC-tandem mass spectrometry, we identified 44 secretory proteins, the
transmembrane protein Msb2, 6 secretory pathway-associated proteins, and 28
predicted cytosolic proteins. Many secretory proteins are wall-related,
suggesting that their presence in the growth medium is at least partially due to
accidental release from the walls. Als3, Csa2, Rbt4, Sap4, and Sap6 were
enriched in the medium of hyphal cultures; Bgl2, Cht3, Dag7, Eng1, Pir1, Rbe1,
Scw11, Sim1/Sun42, Xog1, and Ywp1 in the medium of yeast cells; and Plb4.5
in pH 4-medium. Seven proteins (Cht3, Mp65, Orf19.5063/Coi1, Scw11, Sim1,
Sun41, and Tos1) were consistently present under all conditions tested. These
observations indicate that C. albicans tightly regulates its secretome. Mp65,
Sun41, and Tos1 were each predicted to contain at least one highly
immunogenic peptide. In total, we identified 29 highly immunogenic peptides
originating from 18 proteins, including two members of the family of secreted
aspartyl proteases. Fifty-six peptides were identified as proteotypic and will be
useful for quantification purposes. In summary, the number of identified
secretory proteins in the growth medium has been substantially extended, and
growth conditions strongly affect the composition of the secretome.
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Introduction
Candida albicans is commonly found as a benign commensal in many warm-
blooded animals. In humans it mainly resides on the skin and on mucosal
surfaces without causing significant harm to the host. But under certain
circumstances, such as a weakened host immune system, epithelial damage, or
disturbance of the microbial gut flora, C. albicans can cause superficial to deep-
seated mucosal infections. When the immune system of the host is severely
compromised, for example, during HIV infection, by chemotherapy or after
organ transplantation, the fungus can penetrate the tissue even further and gain
access to the bloodstream, which causes life-threatening systemic infections.
Several factors contribute to the pathogenic nature of Candida albicans (6). A
major virulence factor is the ability of C. albicans to switch from yeast to
hyphal growth. Loss of this ability leads to complete avirulence in a mouse
model of systemic infection (24). The wall and especially the covalently
anchored wall proteins are important contributors to pathogenicity as well. They
mediate adherence and invasion of host cells, promote biofilm formation, and
protect against the immune system (19). Secreted hydrolytic enzymes, like
lipases and proteases, play a role in tissue degradation. In addition, they
facilitate nutrient acquisition and invasion (37). Identification of other secreted
proteins could determine novel virulence factors. The identification of secreted
proteins could furthermore be of importance with regard to the development of
clinical markers or vaccine candidates.
Proteins in the growth medium that follow the classical secretory pathway are
marked for secretion by an N-terminal signal sequence. However, some proteins
have been identified in the medium of C. albicans that do not possess this
typical signal for secretion, raising the question if they reach the extracellular
space via an alternative route (29). A genome-wide computational study, based
on predicting the presence of a signal peptide, has identified 283 potentially
secreted proteins. Using mass spectrometric analysis of the secretome of C.
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albicans grown under four different growth conditions, we identified 44
secretory proteins, a soluble form of the transmembrane protein Msb2, six
proteins predicted to be associated with compartments of the secretory pathway,
and 28 cytosolic proteins in the growth medium of Candida albicans, thereby
confirming and considerably extending earlier studies (15, 25, 47).
Additionally, we present evidence that many covalently anchored wall proteins
are partially released into the growth medium. We show further that the protein
composition of the secretome changes considerably in response to
environmental conditions. Interestingly, we identified a core set of seven
proteins that are found under all conditions tested. Most of the genes belonging
to this core set are highly conserved among other fungi, underlining their
functional importance. Finally, using the immunoinformatics algorithm POPI,
we identified a number of peptides that are predicted to elicit a strong response
in one or both arms of the immune response and thus might be valuable targets
for vaccine development.
Materials and methods Strains and growth conditions
Chemicals were obtained from Sigma-Aldrich unless otherwise stated. C. albicans
SC5314 (13) was used throughout this study. C. albicans was pre-cultured in liquid
YPD medium (10 g/l yeast extract, 20 g/l peptone and 20 g/l glucose) in a rotary shaker
at 200 rpm and 30°C overnight. The overnight culture was used to inoculate flasks
containing 50 ml YNBS (6.7 g/l YNB, 20 g/l sucrose, and 75 mM MOPSO [3-(N-
morpholino)-2-hydroxypropanesulfonic acid] set at pH 7.4 or 75 mM tartaric acid set at
pH 4 at an initial OD600= 0.05. These cultures were incubated for 18 h at 30 or 37°C and
shaken at 200 rpm. For hyphal induction, the culture medium was supplemented with 5
mM N-acetylglucosamine (GlcNAc).
Analysis of overnight cultures
For morphological analysis, the cells were visualized by light microscopy and
photographed. For determination of the biomass, the cultures were spun down after 18 h
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of growth and the pellet was dried at 60°C and weighed. To isolate the proteins from the
growth solution, the cultures were spun down and the supernatant was centrifuged again
to remove remaining cells. The medium was concentrated using 10-kDa cutoff filters
(Amicon Ultra-15 Centrifugal filter units, Millipore). The whole procedure was
performed at 4°C. After concentration, the medium proteins were quantified using the
BCA assay with bovine serum albumen as a standard (41). The amount of protein was
normalized to biomass dry weight.
Mass spectrometry of growth solution proteins
The concentrated proteins from the growth medium were reduced with 10 mM
dithiothreitol in 100 mM NH4HCO3 (1 h at 55 C). After cooling to room temperature,
the protein solutions were transferred to 10-kDa cut-off spin filter (Millipore) tubes and
centrifuged. The reduced proteins were alkylated with 65 mM iodoacetamide in 100
mM NH4HCO3 for 45 min at room temperature in the dark. The samples were quenched
were washed six times with 50 mM NH4HCO3 and either frozen in liquid nitrogen and
stored at -80 C or directly digested using 2 μg Trypsin Gold (Promega, Madison,WI)
from a 1 μg/μl stock solution for 18 h at 37°C. The tryptic digests were desalted using a
C18 tip column (Varian, Palo Alto, CA) according to the manufacturer’s instructions
and the peptide concentration was determined at 205 nm using a NanoDrop ND-1000
(Isogen Life Science, IJsselstein, The Netherlands) (9). Each sample was diluted with
0.1% trifluoroacetic acid to a final concentration of 75 ng/μl, and 10 μl per run were
injected onto an Ultimate 2000 nano-HPLC system (LC Packings, Amsterdam, The
Netherlands) equipped with a PepMap100 C18 reversed phase column (75 μm inner
diameter, 25 cm length; Dionex, Sunnyvale, CA). We used an elution flow rate of 0.3
μl/min along a linear gradient with increasing acetonitrile concentration over 45 min.
The eluting peptides were directly ionized by electrospray in a Q-TOF (Micromass,
Whyttenshawe, United Kingdom). Survey scans were acquired from m/z 350-1200. For
low energy collision-induced dissociation (MS/MS), the most intense ions were selected
in a data-dependent mode.
Analysis of mass spectrometric data
The generated spectra were processed using the MaxEnt3 algorithm included in the
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Masslynx Proteinlynx software. The resulting pkl (peak list) files were submitted to an
internally licensed version of MASCOT (Matrix Science, Great Britain) using both a
complete C. albicans proteome database derived from the complete ORF translation
from the Candida Genome Database (2) and a dedicated database of GPI anchored and
signal peptide-containing proteins with 143 entries. To generate this database, a
preselected list of potential proteins was subjected to signal peptide prediction using
SignalP3.0 (3). In addition, all potential proteins were analyzed for the presence of a
GPI anchor sequence using the BIG-PI fungal predictor (10). Subsequently, predicted
N-terminal signal peptides and amino acids C-terminal of the predicted -amino acid
involved in GPI attachment were removed from the database. In MASCOT two
miscleavages and a tolerance of 0.6 Da for peptides and MS/MS were allowed.
Probabilistic MASCOT scoring was used to evaluate the identified peptides and
proteins. A P value of <0.05 was considered significant for peptide identification. Four
to six independently obtained biological samples were analyzed for each condition
(biological replicates). Each biological sample was subjected to three runs with MS/MS
selection switching times of 2 s, 1.5 s, and 1.25 s, respectively. For a semi-quantitative
analysis of our data, we calculated for each growth condition the mean of the total
number of peptide identifications per biological replicate.
Peptides identified in at least 50% of all runs in a single condition were considered to be
proteotypic (27) (see also Supplemental Table S5 and S6 for details). The
immunogenicity of peptides was predicted using the POPI 2.0 web server (50).
All Supplemental materials can be found online under the following link:
http://onlinelibrary.wiley.com/doi/10.1002/yea.1775/suppinfo
Results and discussion
Selection of growth conditions for secretome analysis
As C. albicans is known to acidify its environment (49), a stable pH requires
buffering of the culture medium. For cultures grown at pH 4, we selected
tartaric acid as a buffer. It is not metabolized by C. albicans (data not shown)
and has two pKa values, one at 3.01 and the other at 4.37, which makes it
suitable for buffering at pH 4. To buffer cultures at pH 7.4, we used MOPSO,
which has a pKa of 6.90 at 37ºC. It is a hydrophilic molecule, which minimizes
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its uptake by the cell in its uncharged form. We used buffer concentrations of 75
mM, which kept the pH stable throughout the overnight culturing period used
(data not shown). Elevated glucose concentrations inhibit hyphal growth and
activate the glucose repression pathway leading to the repression of many
genes, including several genes involved in the utilization of alternative carbon
sources (26, 36). To avoid glucose repression, we used sucrose as a carbon
source. Sucrose does not affect hyphal growth and allows the expression of
glucose-repressed genes such as HEX1, which encodes a secretory N-
acetylglucosaminidase (33), and MAL2, which encodes an -glucosidase
(maltase) (12). Importantly, in contrast to S. cerevisiae, C. albicans does not
secrete an invertase to hydrolyze sucrose extracellularly but uses a H+/sucrose
symporter to transfer it over the plasma membrane, and hydrolyzes it
intracellularly using Mal2 (53).
Table1. Morphology, biomass production, and medium protein concentration of overnight cultures grown under various conditions. Averages of at least three cultures are shown (Coefficient of Variation 25%). Growth conditiona
Morphology of overnight cultures
Biomass mg/ml
Medium protein g/mg biomass
pH 7.4, 37ºC Yeast and hyphae 2.2 0.83 pH 7.4, 37ºC + 5 mM GlcNAc
Mainly hyphae 2.0 2.32
pH 7.4, 30ºC Exclusively yeast cells 2.8 0.98 pH 4.0, 37ºC Exclusively yeast cells 3.3 0.87 aYNB containing 2% sucrose as carbon source.
To establish if the composition of the C. albicans secretome depends on growth
conditions, we selected conditions that were expected to result in a distinct
protein expression and morphology (Table 1) (4, 14, 39, 45, 52). When grown
overnight at pH 7.4 and at 37°C the culture consisted of a mixture of yeast and
hyphal cells. In the presence of GlcNAc, hyphal growth predominated (data not
shown). When the temperature was decreased to 30°C or the medium pH
lowered to 4, the cultures consisted exclusively of yeast cells.
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After concentration of the C. albicans culture supernatants, their protein
contents were determined and normalized to the biomass of the cultures. Table
1 shows that growth was optimal at pH 4 and 37ºC and that hyphal growth
resulted in diminished biomass formation. Except for the GlcNAc-
supplemented culture, the protein content of the culture supernatants was
similar (0.8 – 1.0 g protein/mg biomass (dry weight) corresponding to about
0.1% of the total biomass). The growth medium of GlcNAc-induced cultures
contained about 2.3 g protein/mg biomass, suggesting that hyphae either
secrete more proteins or are more sensitive to shearing forces occurring in
shaken cultures.
Composition of the Candida albicans secretome
The number of predicted secretory proteins (proteins with an N-terminal
secretory signal sequence but without an internal transmembrane sequence and
mitochondrial signal sequence) for C. albicans is 333 (21), including 50
predicted GPI proteins, which are believed to become tail-anchored to the
plasma membrane or the cell wall (8). Under our growth conditions, we
identified a total of 44 secretory medium proteins. Interestingly, twenty-nine of
them have a cell wall-related function or location, including eighteen GPI-
proteins that have been described as being covalently anchored to the cell wall
(19). This is consistent with earlier studies of C. albicans and Candida glabrata
in which also known GPI wall proteins were found in the culture solution (44).
As our cultures were shaken at 200 rpm, it seems possible that non-covalently
bound wall-associated proteins such as Bgl2, Cht1, Cht3, Eng1, and Xog1 are
partially washed out of the walls. Wall proteins known to be covalently bound
to the wall polysaccharides, such as GPI proteins, Pir1, Scw11, Sim1/Sun42,
and Tos1, might also be partially washed out, namely, after their release from
the plasma membrane but before their covalent attachment to skeletal
polysaccharides. Release might also take place during cell wall remodeling, for
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example, during isotropic growth. This hypothesis is supported by the
identification of -1,3-glucan-associated forms of the wall proteins Als3 and
Hyr1 in the supernatant of C. albicans cultures (48). In addition to the wall-
related proteins, fifteen secretory proteins were identified without a known
wall-related function or location, including five members of the Sap (secreted
aspartyl protease) family, a glucoamylase, a hexosaminidase, and a
phospholipase. A fragment of Msb2, a transmembrane protein located in the
plasma membrane (for further discussion see below), and six proteins predicted
to be associated with intracellular compartments of the secretory pathway were
also found. Finally, 28 predicted cytosolic proteins were identified; many of
which are known to be highly abundant intracellularly (Supplementary Tables
S1-4) (20).
Proteotypic peptides are defined as peptides that are observed in at least 50% of
all corresponding protein identifications in mass spectrometry-based
proteomics; they are responsible for the majority of protein identifications (27).
Since we performed 12-18 LC-MS/MS runs per condition, we have a sound
basis to recognize proteotypic peptides. We identified 56 proteotypic peptides in
23 proteins with up to 6 proteotypic peptides per protein (Supplemental Tables
S5 and S6). An important use of proteotypic peptides is absolute quantification
of proteins (27).
Dynamics of the Candida albicans secretome
Because the total number of peptide identifications of a particular protein is
correlated with the concentration of that protein (22), we calculated for each
protein the average number of peptide identifications/biological replicate under
the four growth conditions studied (Table 2). This semi-quantitative approach
shows that different modes of growth such as yeast or hyphal growth or certain
conditions such as low pH lead to clear differences in the protein composition
of the growth solution (Tables 2 and 3). Seven proteins (Cht3, Mp65,
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Orf19.5063/Coi1, Scw11, Sim1/Sun42, Sun41, and Tos1) were found under all
four growth conditions tested when “the mean 1 in all four conditions” was
used as the threshold value. Notice, however, that the concentrations of Cht3,
Scw11, and Sim1/Sun42 were considerably decreased in hyphal cultures.
Importantly, we identified almost all predicted tryptic peptides of Mp65,
Sim1/Sun42, and Sun41 that were in the detection range of our instrument,
suggesting that they are abundant medium proteins. This is also consistent with
their high Codon Adaptation Index values of 0.65, 0.70, and 0.61, respectively
(Candida Genome Database, http://www.candidagenome.org).
Table 2. Mass spectrometric analysis of the proteins released into the growth medium under various environmental conditions. Y, exclusively yeast cells; H, predominantly hyphal growth; Y + H, both growth forms present in considerable amounts. Protein Properties and functiona No. of
PPb
Mean of peptide identifications in the biological replicatesc
pH 7.4 37°C Y+H
pH 7.4 37°C +GN
H
pH 7.4 30°C
Y
pH 4 37°C
Y Wall-related proteins Als3 GPI-WP, adhesin 3 1.0 6.5 0 0 Als4 GPI-WP, adhesin 0 0 0 0.2 0 Bgl2 Transglucosylase 2 3.0 0.3 4.2 7.4 Cht1 Chitinase 1 0 0 2.8 3.0 Cht2 GPI-WP, chitinase 1 0.8 3.7 2.8 1.6 Cht3 Chitinase 3 8.2 1.3 10.2 8.4 Crh11 GPI-WP, transglycosylase 0 0.4 0 0 0 Ecm33 GPI-WP, wall integrity 0 2.0 0 0.8 1.6 Eng1 Endo-1,3- -glucanase 3 3.8 0 8.0 5.6 Fgr41 Pga35, GPI protein 0 0.2 0 0.2 1.4 Mp65 Transglycosylase 6 13.2 10 14.5 15.4 Pga4 GPI-WP, transglucosidase 1 0.8 0 1.0 2.0 Pga45 GPI-WP, unknown 0 0.4 0.3 0.2 0.4 Phr1 GPI-WP, transglucosidase 0 0.2 0 0 0 Pir1 Wall cross-linking protein 1 1.2 0 1.5 3.6 Rbt1 GPI-protein, Flo11
domain 0 0.2 0 0 0
Rbt5 GPI-WP, acquisition of hemoglobin
1 0.6 0.3 2.5 1.8
Rhd3 Pga29, GPI-WP 0 0 0 0 0.4 Sap10 GPI-WP, protease 0 0 0 0 0.8 Scw11 1,3- -Glucanase 5 10.6 1.3 10.2 8.4
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Sim1 Sun42, wall maintenance 3 7.0 1.8 9.2 11.6 Sod4 GPI-WP, superoxide
dismutase 0 0.2 0 0 0
Sod5 GPI-WP, superoxide dismutase
0 0 0.7 0 0
Ssr1 GPI-WP, wall structure 1 1.2 0 0 2.8 Sun41 Wall maintenance 4 9.2 6.0 10 12.2 Tos1 Unknown 6 10.4 8.7 11.8 13.6 Utr2 GPI-WP, glycosidase 3 3.4 0.5 0 8.0 Xog1 Exo-1,3- -glucanase 2 10 0.8 10 7.6 Ywp1 GPI-WP 0 3.6 0 2.2 2.6 Other proteins Ape2d Metallo-aminopeptidase 0 0 0.2 0 0 Csa2 CFEM domain 0 0.6 1.7 0 0 Cyp5d Peptidyl-prolyl cis-trans
isomerase 0 0.2 0.7 0.2 0
Dag7 Unknown 1 1.8 0 2.8 3.8 Gca1 Glucosyl hydrolases 0 0.4 0 0.2 1.2 Hex1 Hexosaminidase 0 0.2 0 0 0 Kar2 d Chaperone-like protein 0 0 0.7 0 0 Mnt1d 1,2-mannosyl transferase 0 0.4 0 0 0 Msb2 Putative sensor protein 0 2.0 0.7 1.2 0.2 Op4 Opaque-specific 0 0 0 0 0.8 Orf19. 5063e
Ciclopirox Olamine-Induced
3 7.0 3.3 7.2 1.6
Pdi1d Protein disulfide-isomerase
0 1.0 0 0 0
Plb4.5 GPI-protein, phospholipase
1 0 0 0 6.0
Pra1 Immune evasion protein 0 0.2 0 0 0 Pry1 Opaque-specific,
SCP_PRY_like domain 0 0 0 0 0.4
Rbe1 SCP_PRY_like domain 0 1.6 0 3.5 1.2 Rbt4 SCP_PRY_like domain 3 0.8 6.8 2.0 0.2 Sap4 Secreted aspartyl protease 1 0 6.2 0 0 Sap5 Secreted aspartyl protease 0 0.2 0.3 0 0 Sap6 Secreted aspartyl protease 1 0 9.2 0 0 Sap8 Secreted aspartyl protease 0 0 0 0 0.6 Ubi3 0 0.6 1.7 0 0 a CGD, Candida Genome Database; GPI-WP, GPI-anchored wall protein. b PP = Proteotypic peptide; For sequences see Supplemental Table S6. c Mean of the total number of peptide identifications in the biological replicates (n = 4-6) see also Supplementary Tables S1-S4. d Predicted to be ER- and Golgi-associated proteins. e Proposed name: Coi1. GN= GlcNAc; Y=Yeast morphology; H=Hyphal morphology.
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Table 3 further shows that 4-5 proteins are enriched in the growth medium of a hyphal culture (Als3, Rbt4, Sap4, Sap6, and presumably also Csa2). The transcript levels of PIR1, RBE1, and YWP1 rapidly and strongly decline and remain low when YPD-grown yeast cells are transferred to a hyphal induction medium (42). Consistent with this, peptides of Pir1, Rbe1, and Ywp1 are absent in the growth medium of hyphal cultures (GlcNAc-induced hyphal growth) but present in the media of yeast(-containing) cultures. In total, ten proteins are enriched in the media of yeast-containing cultures (Bgl2, Cht3, Dag7, Eng1, Pir1, Rbe1, Scw11, Sim1/Sun42, Xog1,Ywp1). The medium of pH 4-grown cells is clearly enriched in Plb4.5 and probably also, but to a lesser extent, in Fgr41/Pga35, the opaque phase-specific proteins Op4 and Pry1, and the aspartyl proteases Sap8 and Sap10. These observations illustrate the dynamic nature of the secretome. Table 3. Relative enrichment of proteins in the growth solution under various environmental conditions. Conditionsa Characteristic features Secretory proteins All Mp65, Cht3, Orf19.5063/Coi1,
Scw11, Sun41, Tos1b 2 Predominantly hyphae Als3, Csa2, Rbt4, Sap4, Sap6 1+3+4 Mixed culture or
exclusively yeast cells Bgl2, Cht3, Dag7, Eng1, Pir1, Rbe1, Scw11, Sim1, Xog1, Ywp1
4 pH 4 Plb4.5 aGrowth conditions: 1: pH 7.4, 37°C; 2: pH 7.4, 37°C, +5 mM GlcNAc; 3: pH 7.4, 30°C; 4: pH 4, 37°C. bProteins with an average total peptide score in the biological replicates 1.
Discussion of individual secretory proteins in the growth solution
Csa2 is a small secretory protein without a GPI-anchor signal sequence. It has a
CFEM domain, but its function is unknown. Interestingly, it seems to be
enriched in hyphal cultures (Table 3). Fgr41 (Pga35) is a predicted GPI protein;
the encoding gene has been annotated as a possibly spurious ORF (CGD). We
have identified Fgr41/Pga35 in the growth medium in three of the four
conditions tested, showing that the corresponding gene is a genuine ORF.
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Gca1 is a predicted glucoamylase, which is consistent with the observation that
C. albicans can grow on soluble starch as a carbon source (31). Conceivably, it
might also allow C. albicans to use host glycogen as a carbon source.
Hex1 is an N-acetylglucosaminidase. When GlcNAc is used as a carbon source,
Hex1 activity is strongly induced (32). As Hex1 is only found in the growth
medium under a single growth condition (pH 7.4, 37°C) and not in GlcNAc-
supplemented medium, it seems likely that the presence of sucrose prevents the
induction of Hex1 and that GlcNAc primarily acts a hyphal-inducing compound
and does not need to be metabolized for this effect to occur.
Mp65 is found in all four growth media and its level does not seem to change
significantly. This is in agreement with earlier observations indicating that
MP65 is constitutively expressed during yeast and hyphal growth (42).
Msb2 possesses an N-terminal signal peptide. It is described as a sensor of cell
wall damage and is predicted to be a transmembrane protein associated with the
plasma membrane (35). We identified five different peptides that are unique for
Msb2 in tryptic digests of medium proteins, indicating that Msb2 or a processed
form of Msb2 is also present in the culture medium. This is consistent with the
observations by Vadaie and co-workers in S. cerevisiae who found that Msb2 is
processed into medium and cell-associated forms. As a result, a large fragment
of ScMsb2 ends up in the growth medium (51). Interestingly, the peptides
identified by us in CaMsb2 are located closely to each other (1154-1177, 1212-
1219, 1223-1237, 1238-1253, 1254-1290) in a region that is homologous to the
so-called cleavage domain of ScMsb2, consistent with the notion that CaMsb2
and ScMsb2 are functionally related (51).
Op4 and Pry1 are found only in the medium of pH 4-grown cells. Both have
been described as opaque cell-specific, but in view of our results it cannot be
excluded that they are also synthesized by white-phase cells at low pH.
Orf19.5063 is a predicted protein in Assemblies 19, 20, and 21 of the Candida
genome. We found it in the culture medium under all four growth conditions.
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Interestingly, Orf19.5063 is upregulated in the presence of the antifungal
compound ciclopirox olamine, which causes a transcriptional profile resembling
that of iron restriction (38). Therefore we propose the name Coi1 (Ciclopirox
Olamine Induced 1) for Orf19.5063. Intriguingly, Coi1 is conserved only in C.
albicans, C. dubliniensis, C. tropicalis and Lodderomyces elongisporus, which
have all been implicated in causing bloodstream infections in humans.
Plb4.5 is a putative phospholipase B and is predicted to be GPI-anchored. It is
only found in the medium of pH 4-grown cells. Under these conditions nine
different peptides were identified suggesting that it might be an abundant
protein.
Pry1, Rbe1, and Rbt4 share a conserved domain (SCP_PRY1_like domain), but
the function of this domain is unknown. Rhd3 is a GPI wall protein that is also
known as Pga29. We detected it only in the medium of pH 4-grown cells. It
does not seem to be strictly correlated with yeast growth because it was absent
in a yeast culture growing at pH 7.4 and 30ºC (Table 2).
The Sap family, which has been extensively investigated, consists of ten
members, two of which are wall-bound GPI proteins (Sap9 and Sap10), whereas
the others are secreted into the growth medium (30). The subfamily SAP4 to
SAP6 is known to be coordinately expressed with hyphal growth and in
accordance with this we found Sap4 and Sap6 (and to a much lesser extent
Sap5) in the medium of hyphal cultures, but not in the media of yeast cultures
(Tables 2 and 3). Interestingly, Sap 8 and the GPI-modified Sap10 are only
found in pH 4-grown cell cultures. The Sap family thus represents a clear
example of the adaptability of the secretome.
Sim1 (Sun42) and Sun 41 both belong to the Sun family and share the so-called
SUN domain. The transcript levels of SIM1/SUN42 strongly decrease during
hyphal growth (11, 17), consistent with our observation that the level of Sim1 in
the medium of a predominantly hyphal culture is much lower than in
(predominantly) yeast cultures.
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Finally, Ape2, Cyp5, Kar2, Mnt1, and Pdi1 each possess a predicted N-terminal
signal peptide or a transmembrane domain close to the N-terminus and are
believed to be associated with the endoplasmic reticulum or the Golgi apparatus
(5, 40).Their presence in the medium is consistent with the observation that the
culture medium of C. albicans contains membrane vesicles (1). Table 2 shows
that they are mainly found in the medium of (partially) hyphal cultures, and are
almost completely absent in yeast cultures, suggesting that their presence in the
medium is due to hyphal breakage. Intriguingly, Ubi3 also possesses a predicted
N-terminal signal peptide or N-terminal transmembrane domain, raising the
question whether this predicted ribosomal protein might be associated with the
rough endoplasmic reticulum.
Identification of peptides with high immunogenic potential
All identified tryptic peptides were subjected to a prediction of their potential to
induce the proliferation of cytotoxic (CTL) and helper T-cell lymphocytes
(HTL) (Table 4) (50). In our complete set of 228 peptides, 29 (~13%) show a
high immunogenic potential, while 77 (~34%) show no immunogenic potential
at all whereas the remainder had an intermediate potential (Table 4,
Supplemental Table S6).
Mp65, which seems to be an abundant medium protein under all growth
conditions tested, also contains a predicted highly immunogenic peptide
(LYGVDCDQVSAVLK). This result was consistent with the predicted
antigenicity of this peptide by another algorithm
(http://bio.dfci.harvard.edu/Tools/antigenic.html). Based on mouse vaccination
studies, Mp65 seems indeed a promising vaccine candidate (34). Sim1/Sun42
and Sun 41 are functionally redundant and the double deletant is nonviable (11).
As the SUN domain of both proteins contains peptides with a high predicted
immunogenicity (Table 4), this domain also seems an attractive vaccine
candidate.
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Table 4. Predicted immunogenicity of secretory protein peptides. Protein Sequence (position) Immunogenicitya
CTLb HTLc Als3/5 APFTLR (306-311) 3 0
Cht2 LSSAIEEIK (259-267) 3 1 Eng1 ELAANIAATVK (797-807)
DASNPSADDTYFPVSR (932-947) 2 3
3 1
Gca1 LNVHIEPTDLTDVFVLPEELVVKPK (108-132) GHSITGLGESIHGSLNEPGVVK (193-214) YFDNPVHPPFEVGYSGSDYPLGFDK (479-503)
3 0 3
0 3 0
Mp65 LYGVDCDQVSAVLK (161-174) 1 3 Msb2 SALNYPFVVENSISSAQIFQYLPR (1154-1177)
ALGSFITTPGSAIYR (1223-1237) 3 3
3 2
Pga4 AGIYVILDVNTPHSSITR (99-116) 3 1 Pga45 DANTEQTIEGILK (86-98) 0 3 Rbt4 LGCAYK (312-317)
SYMAENVLRPQ (348-358) 2 2
2 2
Sap4/6 TLSVGLR (269-275, 270-276) 0 3 Sap4 LSVIVDTGSSDLWVPDSNAVCIPK (102-125)
YADGSVAQGNLYQDTVGIGGVSVR (159-182) 0 0
3 3
Sap6 GNLYQDTVGIGGASVK (168-183) 0 3 Sim1 TDYPGSENMNIPTLLSAGGK (233-252)
TSTQYYVNNAGVSVEDGCIWGTEGSGVGNWAPVVLGSGTTGGK (271-313)
3 0
3 3
Sod5 HGNIMGESYK (118-127) TEYDDSYISLNEK (128-140)
2 2
2 3
Sun41 IVGESGSTVSGSCSYANGK (376-394) 0 3 Tos1 DSYYTPGSTDNCVFLNYHGGSGSGVWSAK (231-259) 0 3 Utr2 EIYATAYDIPNDVK (297-310) 2 2 Xog1 QISNLGLNFVR (120-130)
DSYNFQNGDNTQVTLNVLNTIFK (189-211) QFFLDGYNSLR (243-253)
3 2 3
2 2 1
Ywp1 VINVPAR (87-93) 3 0 a POPI algorithm (50); 3: PD50 < 1 nM; 2: PD50 = 100 nM - 1 nM; 1: PD50 = 10 mM - 100 nM; 0: PD50 >10 mM, in which PD50 = Protective Dose that protects 50% of the animals challenged b Cytotoxic T-lymphocytes, c Helper T-lymphocytes
Concluding remarks
We have analyzed the proteins of C. albicans that are released into the growth
medium under various environmental conditions. This allowed us to compare
yeast and hyphal cultures and the effect of pH. The polypeptide content of the
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growth medium was 0.1% of the total biomass for three of the four conditions
tested, but was >2-fold higher in the hyphal culture (Table 1). In total we
identified 44 secretory proteins, which is considerably more than in earlier
studies. Twenty-nine of them had a wall-related location or function, whereas
15 possessed a function unrelated to the cell wall. We also detected a soluble
form of the plasma membrane sensor protein Msb2 and six proteins predicted to
be associated with early compartments of the secretory pathway. Conceivably,
some of the wall-related proteins found in the culture solution could be involved
in biofilm formation and, in particular, in the formation of extracellular
polysaccharides (15). In total, we detected 28 predicted cytosolic proteins in the
various culture solutions (Supplementary Tables S1-4). Interestingly, in pH 4-
grown yeast cultures we did not identify any cytosolic protein whereas in the
hyphal culture we identified considerably more cytosolic proteins than in the
other cultures, suggesting that in comparison to yeast cells hyphae are more
liable to breakage due to the shearing forces inherent to shaking flask cultures.
We cannot exclude that medium proteins are degraded over time. However, we
found many more tryptic peptides than semitryptic peptides (peptides that match
trypsin specificity only at one terminus), suggesting that proteolytic degradation
was limited (data not shown). Albuquerque and co-workers have described
membrane-bound vesicles in the culture medium of Histoplasma capsulatum
and other ascomycetous fungi including C. albicans (1). Interestingly, when the
culture medium is filtered using a 200-nm filter, the number of cytosolic
proteins in the filtrate is negligible whereas the number of secretory proteins
does not seem to be affected (unpublished data). This suggests that the cytosolic
proteins found in the medium are contained in membranous vesicles (1).
Compared to the predicted secretomes (proteins with an N-terminal secretory
signal peptide, including GPI-proteins but excluding proteins with an internal
transmembrane sequence) of other yeasts such as Kluyveromyces lactis (178
proteins) (46), Saccharomyces cerevisiae (163 proteins), Pichia pastoris (88
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proteins) (28), Schizosaccharomyces pombe (66 proteins) (23), C. albicans has
a relatively large predicted secretome. Possibly, the secretomes of non-
pathogenic yeasts tend to be smaller as has also been observed for plant
pathogenic mycelial fungi (7). Alternatively, the higher number of predicted
secretory proteins might be related to the pleomorphic nature of C. albicans.
Importantly, of the 44 secretory proteins we were able to identify in the growth
medium, only Mp65, Sun41, and Tos1 seemed to be consistently and
abundantly present under all four conditions. This observation is supported by
previous studies (15, 25). The corresponding genes are highly conserved in
many fungi, underlining their functional importance. These proteins could
therefore be useful for the development of clinical markers or as vaccine
candidates. Interestingly, a recently developed algorithm for the identification
of immunogenic peptides predicts that Mp65, Sun41, and Tos1 each possess a
highly immunogenic peptide (50).
The composition of the secretome differed considerably between pH 4- and pH
7.4-grown cells and between yeast and hyphal cultures (Tables 2 and 3). This
clearly demonstrates that the composition of the secretome can vary widely. If
our assumption is correct that some of the medium proteins are actually washed-
out wall proteins, the dynamic nature of the wall proteome of C. albicans (16,
43) could partially explain the observed differences. However, we also observed
relative enrichment of specific hydrolytic enzymes in the medium depending on
growth conditions and morphology (Table 3). This is illustrated by the increased
levels of Sap4 and Sap6 in hyphal culture medium and of Plb4.5 at pH 4 (to a
lesser extent the levels of Gca1 and Sap8 also seem to increase at pH 4; see
Table 2). The capability of adapting the composition of the secretome probably
helps C. albicans to better cope with the different growth conditions that it
encounters on the various sites of infection and during the subsequent infection
process. The proposed tight regulation of the composition of the secretome by
C. albicans probably also explains, at least to some extent, why only a limited
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number of the predicted secretory proteins have been identified so far. For
example, we did not identify any member of the extended family of secretory
lipases (18). The most likely explanation is that our growth conditions and in
particular the use of sucrose instead of lipids as a carbon source did not favor
the expression of the lipase genes (18).
Acknowledgements
We thank Dr. Leo de Koning for his stimulating support and advice. F.M.K.
acknowledges the financial support by the EU Program FP7-214004-2
FINSysB.
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