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Applied and Environmental Microbiology, February 2009, p. 1129-1134, Vol. 75, No. 4
0099-2240/09/$08.00+0 doi:10.1128/AEM.01837-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Pichia anomala DBVPG 3003 Secretes a Ubiquitin-Like Protein That Has Antimicrobial Activity
Jessica De Ingeniis,1,2
Nadia Raffaelli,1
Maurizio Ciani,2 and
Ilaria Mannazzu2,3*
Istituto di Biotecnologie Biochimiche, Università Politecnica delle Marche, Via Ranieri, 60131 Ancona, Italy,1
Dipartimento SAIFET sez di Microbiologia Alimentare, Industriale e Ambientale, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy,2
Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agroalimentari, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy3
Received 8 August 2008/
Accepted 16 December 2008

ABSTRACT
The yeast strain
Pichia anomala DBVPG 3003 secretes a killer
toxin (Pikt) that has antifungal activity against
Brettanomyces/Dekkera sp. yeasts. Pikt interacts with β-1,6-glucan, consistent
with binding to the cell wall of sensitive targets. In contrast
to that of toxin K1, secreted by
Saccharomyces cerevisiae, Pikt
killer activity is not mediated by an increase in membrane permeability.
Purification of the toxin yielded a homogeneous protein of about
8 kDa, which showed a marked similarity to ubiquitin in terms
of molecular mass and N-terminal sequences. Pikt is also specifically
recognized by anti-bovine ubiquitin antibodies and, similar
to ubiquitin-like peptides, is not absorbed by DEAE-cellulose.
However, Pikt differs from ubiquitin in its sensitivity to proteolytic
enzymes. Therefore, Pikt appears to be a novel ubiquitin-like
peptide that has killer activity.

INTRODUCTION
After its initial discovery in
Saccharomyces cerevisiae (
2),
the killer phenotype has been found in yeasts belonging to the
genera
Candida, Cryptococcus, Debaryomyces, Hanseniaspora, Hansenula, Kloeckera, Kluyveromyces, Metschnikowia, Pichia, Rhodotorula, Schwanniomyces, Torulopsis, Trichosporon, Williopsis, and
Zygosaccharomyces (
9,
16,
19,
25,
28,
53,
56). The distribution of this character
among natural yeast isolates and in laboratory strains is accompanied
by killer toxins with large biodiversity, in terms of their
biochemical characteristics, genetic determinants, and spectra
of action (
25). In spite of this diversity, all known killer
toxins are proteins (
1,
31) or glycoproteins (
5,
11,
28,
43,
54) that kill sensitive cells via a two-step mode of action.
During the first step, the killer toxin binds a receptor site
on the cell wall of its sensitive target. In the second step,
which has been far less characterized, the killer toxin is assumed
to interact with receptors on the cell membrane and to kill
the sensitive cells via different mechanisms. These include
cell membrane permeabilization, cell cycle perturbation, inhibition
of DNA synthesis, and inhibition of β-1,3-glucan synthetase
activity (
7,
14,
15,
41,
49,
53).
As the spectrum of action of some toxins has extended to microbial pathogens of clinical interest, killer toxins and/or killer toxin-like antibodies and mimotopes are of great relevance to medicine (8, 25). Other toxins that exert a killing action on spoilage yeasts have interesting applications in the fermentative (46) and food and feed industries (10, 11, 12, 23, 32, 44), where they can be used as "natural" food antimicrobials.
In a previous study, we showed that Pichia anomala DBVPG 3003 produces a killer toxin (known as Pikt) that is active against Dekkera/Brettanomyces sp. yeasts (12). These yeasts can develop in white and red wines, resulting in unpleasant odors and tastes (18). Thus, they represent a major problem in the wine industry. Pikt is stable at acidic pH and in a range of temperatures between 20°C and 40°C (12), as are other toxins produced by different strains of P. anomala (25, 26, 37). Moreover, Pikt maintains its killing activity for at least 10 days in wine. Thus, it shows potential applications as a natural antimicrobial in the wine industry (12).
The present study investigates the mode of action of Pikt and the biochemical properties of the purified protein.

MATERIALS AND METHODS
Yeast strains, media, and growth conditions.
The yeast strains used in this study are listed in Table
1.
The media were YEPD (1% yeast extract, 2% glucose, 2% peptone,
and 1.8% agar when required) for medium-term storage at 4°C,
YEPD
pH 4.4 (YEPD with 100 mM citrate-phosphate buffer, pH 4.4,
for Pikt production), YEPD
pH 4.5 (YEPD with 100 mM citrate-phosphate
buffer, pH 4.5, for K1 production), YEPD
pH 6 (YEPD with 50 mM
Na-phosphate buffer, pH 6, for the production of the
K. lactis killer toxin), GYNB
pH 4.4 (2% glucose, 0.67% yeast nitrogen
base, with 100 mM citrate-phosphate buffer, pH 4.4, for Pikt
purification), and malt agar (Difco, Voigt Global Distribution
Inc., Lawrence, KS) buffered as indicated above for the well
test assay.
P. anomala DBVPG 3003 and
S. cerevisiae DBVPG 6497
were grown at 20°C with shaking (150 rpm).
Kluyveromyces lactis DBVPG 6727 was grown at 25°C with shaking (200 rpm).
Killing assays.
Well test assays were carried out as described by Woods and
Bevan (
52). Briefly, 70 µl of toxin samples was filter
sterilized through 0.45-µm-pore-size membrane filters
(Millipore Corp., Bedford, MA) and then loaded into wells (7-mm
diameter) cut in malt-agar plates that had previously been seeded
with 10
5 cells ml
–1 of a strain sensitive to the toxin.
The killing activity was evaluated as the diameter of the zone
of inhibition around the wells after incubation for 72 h at
20°C and was defined as the mean zone of inhibition of replicate
wells. The linear relationship observed between the logarithm
of killer toxin concentration and the diameter of the inhibition
halo from the well test was used to define Pikt activity in
arbitrary units (AU). One AU was defined as the amount of toxin
contained in 70 µl that generated an inhibition halo of
8 mm. One AU corresponds to about 10 ng of killer protein.
Toxin production.
The killer toxins were produced in 1.0 liter of YEPD buffered as required. After 48 h of growth, the culture broths were centrifuged (5,000 x g for 10 min at 4°C), and the supernatants were microfiltered through 0.45-µm membranes (Millipore Corp., Bedford, MA) and concentrated 100-fold by ultrafiltration (stirred ultrafiltration cells; Millipore Corp., Bradford, MA) with a 3-kDa cutoff membrane for Pikt and a 10-kDa cutoff membrane for K1 and the toxin produced by K. lactis.
Purification of Pikt.
Pikt was produced in 20 liters of GYNBpH 4.4. After 48 h of growth, the culture broth was microfiltered through a 0.2-µm membrane (Schleicher and Schuell GmbH, Germany), and the cell-free medium was concentrated about 350-fold by ultrafiltration with a 5-kDa cutoff membrane (Schleicher and Schuell GmbH, Germany). The concentrated sample was then diluted 10-fold with buffer A (10 mM citrate-phosphate, pH 4.4, 15% glycerol) and concentrated again as described above, to a final volume of about 60 ml. Microfiltration and ultrafiltration were performed using a Bioflex 50 (Schleicher and Schuell GmbH, Germany). The concentrated sample was loaded onto a DEAE-Sepharose Fast Flow (Pharmacia Biotech, Uppsala, Sweden) column (2.5 cm by 7.0 cm) equilibrated with buffer A. The void volume (60 ml) containing Pikt was applied to a Macro-Prep High S Support (Bio-Rad Laboratories, Hercules, CA) (2.5 cm by 6 cm) column equilibrated with the same buffer. After a washing with buffer A, the elution was performed with buffer A containing 1.0 M NaCl. The active fractions were pooled and dialyzed against buffer A. The dialyzed pool was applied to a fast-protein liquid chromatography column of Resource S (1 ml) (Pharmacia Biotech, Uppsala, Sweden) equilibrated with buffer A. The column was washed with the same buffer and eluted with a linear gradient of NaCl, from 0 M to 1.0 M, in buffer A.
Electrophoresis.
Tricine sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was carried out as described by Schagger and von Jagow (38). Before the gels were loaded, the samples were concentrated either by ultrafiltration on a Centricon YM3 membrane (Millipore Corp., Bedford, MA) or by precipitation as described by Wessel and Flugge (50). After being fixed with 5% glutaraldehyde for 1 h, the proteins were silver stained (Sigma Aldrich Inc., St. Louis, MO).
N-terminal amino acid sequencing.
After electrophoresis, Pikt was electroblotted onto a polyvinylidene difluoride membrane. The transfer was performed at 4°C for 1 h at 250 mA, in 10 mM CAPS (3-cyclohexylaminopropanesulfonic acid), pH 11.0, and 10% methanol. After membrane staining with Coomassie brilliant blue R-250, the Pikt band was excised and subjected to N-terminal sequencing by automated Edman degradation on a Procise model 491 sequencer (Applied Biosystems, Foster City, CA).
Immunoblotting.
After the electroblotting, the polyvinylidene difluoride membranes were incubated with antiubiquitin (whole antiserum) developed in rabbits using bovine red blood cell ubiquitin as the immunogen (Sigma Aldrich Inc., St. Louis, MO). Incubations were carried out for 2 h at a 1:100 dilution of the antibody. Horseradish peroxidase-conjugated goat anti-rabbit immunoglobulin G was used as the secondary antibody. Blots were developed by chemiluminescence with the trial kit SuperSignal West Pico (Pierce, Rockford, IL).
Protease treatment.
Twenty nanograms of ubiquitin from bovine erythrocytes (Sigma Aldrich Inc., St. Louis, MO) and purified Pikt were treated with 0.04 U of protease XIV and pepsin (Sigma Aldrich Inc., St. Louis, MO) and incubated for 24 h at 20°C in 100 mM citrate phosphate buffer, pH 4.4.
Identification of the cell wall putative binding site for the P. anomala killer toxin.
The sensitive S. cerevisiae DBVPG 6500 strain (105 cells ml–1) was treated with the killer toxin (30 AU) in the absence or presence of 9 mg ml–1 of the following cell wall polysaccharides: mannan (from S. cerevisiae), glucan (from baker's yeast), laminarin (from Laminaria digitata), and pullulan (from Aureobasidium pullulans), which were all purchased from Sigma Aldrich Inc., St. Louis, MO, and pustulan (from Umbilicaria papullosa; Calbiochem, San Diego, CA). The binding of the toxin to the polysaccharides, as a function of the residual killer activity in solution, was evaluated by the well test after 24 h of incubation at 20°C.
Killer toxin mode of action.
The sensitive S. cerevisiae DBVPG 6500 strain was cultivated in YEPD buffered at the optimal pH of each toxin, and 105 cells ml–1 were incubated at 20°C with 46 AU of K1 or Pikt or at 25°C with 46 AU of Klkt (name given the toxin produced by K. lactis DBVPG 6727), in a final volume of 3 ml. Immediately after toxin addition (time zero) and after 4, 8, and 24 h, 100 µl of the cell suspensions was subjected to viable plate counts. Flow cytometry analyses were performed with an Epics XL (Beckman Coulter, Inc., Fullerton, CA) equipped with a 15-mW air-cooled argon-ion laser (emission, 488 nm) and five sensors for the detection of forward and side light scatter: green (525 nm, channel 1), yellow (575 nm, channel 2), and orange-red (620 nm, channel 3) fluorescence. Size calibration was performed using the flow cytometry size calibration kit (Molecular Probes, Inc., Eugene, OR). Yeast cells were harvested at various times (see Fig. 2), and ethanol-treated cells (70%, 2 h) were included as the positive control for membrane permeability. The samples were then washed and resuspended in PBS (8 mM Na2HPO4, 1.47 mM KH2PO4, 137 mM NaCl, 2.7 mM KCl) to a final concentration of 1 x 105 to 2 x 105 cells ml–1. Fifty microliters of a propidium iodide (PI) stock solution (1 mg ml–1) in PBS was added to 500 ml of cell suspension just prior to the analysis. The fluorescence was detected in fluorescence channel 3. At least 1.5 x 104 cells were analyzed for each experiment. The data were visualized using the WinMDI flow cytometry software (Joseph Trotter, Salk Institute for Biological Studies, La Jolla, CA).

RESULTS
Pikt interacts with β-1,6-glucans.
To identify the putative binding site for Pikt on the cell wall
of the sensitive target, the abilities of various cell wall
components to complex with, and inactivate, the killer toxin
were evaluated. To achieve this, 30 AU of Pikt was mixed with
glucans, pullulan, pustulan, laminarin, and mannan in citrate-phosphate
buffer, pH 4.4, and the residual killer activity was evaluated
by a well test on the sensitive
S. cerevisiae DBVPG 6500 strain.
The results obtained showed that pustulan (β-1,6-glucan)
inhibited its killing activity (Fig.
1). These results were
further confirmed by viable plate counts using 10
5 ultrafiltered
cells (UFC) of the sensitive strain DBVPG 6500. The plate counts
indicated that, in the presence of Pikt plus pustulan, the growth
of the target cells was comparable to that of cells not treated
with the toxin (positive control) (values of 30
x 10
5 and 36
x 10
5 UFC, respectively); other plate count values were as follows:
Pikt alone, 0.013
x 10
5 UFC; Pikt plus glucan, 0.04
x 10
5 UFC;
Pikt plus pullulan, 0.25
x 10
5 UFC; Pikt plus mannan, 0.3
x 10
5 UFC; Pikt plus laminarin, 0.38
x 10
5 UFC.
Pikt killing action differs from that of the killer toxin secreted by S. cerevisiae.
To determine the mechanism responsible for Pikt killer activity,
the mode of action of this toxin was compared with those of
the toxins produced by
S. cerevisiae DBVPG 6497 (K1) and
K. lactis DBVPG 6727 (Klkt). DBVPG 6500 cells, which are sensitive
to the three toxins, were treated with 46 AU of Pikt, K1, or
Klkt. The effects of each toxin were evaluated in terms of viability
and membrane permeability to PI. PI penetrates cells with defective
membrane integrity (
13,
27). Thus, the fluorescence emitted
by PI-stained cells provides a measure of membrane permeability
and can serve as an indirect measure of cell death when this
is mediated by alterations in the cell membrane. While the viable
plate counts indicated that K1 killed the sensitive cells within
4 h, flow cytometry analysis of PI-stained cells confirmed that
the K1 killing activity was mediated by a dramatic increase
in membrane permeability (84.6% ± 4.3% PI-stained cells
after 8 h) (Fig.
2). Klkt took a longer time to kill the sensitive
cells. In particular, 65.0% ± 2.8% of the cells remained
viable 4 h after toxin treatment, and complete killing was observed
at 24 h. At this time, only 18.9% ± 5.71% were permeable
to PI, thus indicating that Klkt killing action is not mediated
by the disruption of the cell membrane. The behavior of Pikt
was similar to that of Klkt with regard to the effects on both
viability (75% ± 2.8% and 3.5% ± 0.21% viable
cells after 4 h and 24 h, respectively) and membrane integrity
of DBVPG 6500 cells (10.7% ± 0.29% of cells permeable
to PI after 24 h of treatment) (Fig.
2).
Purification and N-terminal sequencing of Pikt.
On the basis of the specific interaction between Pikt and β-1,6-glucan, toxin purification was first attempted via affinity chromatography on epoxy-Sepharose 6-B conjugated with pustulan, as already described (36). Contrary to what was expected, Pikt was found to interact very weakly with the resin under any of the conditions tested, resulting in a very low yield (data not shown). Several different chromatographic steps, including hydrophobic interactions and absorption chromatography, were attempted. The best recovery of Pikt was achieved by performing a purification procedure that consisted of two ion-exchange chromatography steps, as outlined in Materials and Methods. The anion-exchange chromatography on the DEAE resin resulted in the recovery of the toxin in the flowthrough of the column, allowing the removal of most of the protein present in the loaded sample. The column flowthrough was loaded directly onto a High S cation-exchange column, and the proteins were eluted isocratically with 1.0 M NaCl. Pikt bound more strongly than other proteins, facilitating purification of a major 8-kDa band by SDS-PAGE (Fig. 3B). The high-molecular-weight product visible in the gel shown in Fig. 3B is also present in samples from the purification procedure which do not contain the killer activity (not shown). To assess the correspondence of the 8-kDa band with the killer toxin, the High S pool was subjected to fast-protein liquid chromatography on a Resource S column, from which the bound proteins were eluted with a continuous NaCl gradient. SDS-PAGE analysis and the killer activity assays on the eluted fractions showed that active fractions again contained the protein corresponding to the 8-kDa band (data not shown). The coelution of the 8-kDa protein with the toxic activity from two different resins (High S and Resource S) and in different experimental conditions (isocratically and with a gradient) confirms the identity of the 8-kDa protein as the killer factor.
Our purification procedure increased specific activity of the
toxin 4,356-fold, with a yield of 41% (Table
2). Starting from
20 liters of culture, the final amounts of purified Pikt were
extremely low and could not be quantified by the Bradford method
(
3). However, they were suitable for the determination of a
partial N-terminal sequence by automated Edman degradation.
The direct determination of the sequence demonstrated that the
N terminus of Pikt was not blocked. Nine of the first 10 residues
were unambiguously identified (MQIFVXTLTG). Similarity searches
using BLASTP did not show any significant homology with known
killer toxins. On the other hand, the sequence of Pikt was identical
to that of
S. cerevisiae ubiquitin (accession number CAA29196).
Pikt is a ubiquitin-like protein.
The similarity of the N-terminal sequence of Pikt with that
of ubiquitin prompted us to determine whether purified Pikt
was recognized by an antiubiquitin antibody. Figure
4 shows
an immunoblot obtained by incubating different fractions from
the purification steps with such an antibody. A positive signal
was evident in all toxin samples, and the corresponding band
migrated exactly like the bovine ubiquitin used as a positive
control. On the other hand, none of the fractions lacking killer
activity cross-hybridized with the antiubiquitin antibody (Fig.
4).
To further investigate the similarity between Pikt and bovine
ubiquitin, both proteins were treated with pepsin and protease
XIV. After proteolytic digestion, the samples were both analyzed
for residual Pikt killer activity and subjected to immunoblot
analysis with the antiubiquitin antibody. As shown in Fig.
5,
only protease XIV completely degraded the toxin. This result
was in agreement with the well test, which highlighted a total
loss of Pikt toxic activity following proteolytic digestion
with protease XIV (
12). Pepsin treatment caused a decrease in
the signal produced by the Pikt-antibody complex, in agreement
with the slight reduction in the activity of the toxin according
to the well test (
12). In contrast, and in agreement with results
described by Schlesinger et al. (
39), neither of the two proteolytic
enzymes degraded bovine ubiquitin.

DISCUSSION
Since Pikt is a secreted toxin, it is possible that it first
acts on the outside of the sensitive cells by interacting with
the cell wall. Accordingly, competitive inhibition of killer
toxin activity by pustulan showed that the toxin selectively
interacts with β-1,6-glucan. Therefore, as has been seen
for the K1 and K2
S. cerevisiae killer toxins (
17) and the toxins
produced by
Hanseniaspora uvarum (
34),
Debaryomyces hansenii (
36), and
Pichia membranifaciens (
35), β-1,6-glucans provide
a putative binding site for Pikt on the cell wall of the sensitive
target. As suggested for other toxins, this first interaction
may be necessary to concentrate the toxin on the cell wall of
the sensitive target and facilitate the contact between the
toxin and the plasma membrane (
40).
To examine the mode of action of Pikt, comparisons were made to K1 and Klkt. K1 is an ionophoric toxin that disrupts membrane integrity (4, 6, 14, 42), while Klkt causes a permanent arrest of the progression of the cell cycle at the G1 phase (7, 24, 51). The behavior of Pikt appeared distinct from that of K1, for both the death kinetics and the membrane permeability. In short, the Pikt killing action is not mediated through the disruption of cell membrane integrity (Fig. 2).
The biochemical characterization of purified Pikt highlighted the similarity to ubiquitin in terms of molecular masses and N-terminal sequences. Moreover, Pikt was specifically recognized by an anti-bovine ubiquitin antibody and, as with ubiquitin and ubiquitin-like peptides, Pikt was not absorbed onto DEAE-cellulose (30). In aggregate, these results support the "ubiquitin-like" nature of Pikt.
Ubiquitin is localized mainly in the cytoplasm. However its presence in the extracellular environment has already been reported. In particular, Kieffer et al. (20) observed that bovine chromaffin cells secrete ubiquitin upon nicotinic stimulation and Vad et al. (45) showed that a Pichia pastoris strain engineered to produce human parathyroid hormone cosecreted ubiquitin in the culture medium.
Interestingly, even though the biological role of secreted ubiquitin needs further investigation, it has been reported that ubiquitin has antimicrobial activity. In particular, Kieffer et al. (20) showed that secreted ubiquitin exerts antibacterial and antifungal activities by destabilizing the fungal cell wall and plasma membrane. Likewise, Yoshio et al. (55) reported that the ubiquitin present in Vernix caseosa, together with other antimicrobial polypeptides, is involved in defense against microbial invasion at birth. Kutty et al. (22) reported that exogenously added ubiquitin inhibits Schizosaccharomyces pombe growth by interfering with cell cycle progression. Kieffer et al. (20) also demonstrated that antimicrobial activity is retained by a short ubiquitin fragment. Accordingly, Purdy and Russel (33) and Kim et al. (21) showed that ubiquitin-derived peptides show antibacterial and antifungal activities in the µM range. Interestingly, Pikt also appears to possess a high specific activity. Indeed, the very small amount of Pikt recovered from 20 liters of cultural broth was characterized by a strong killing action.
One difference between ubiquitin and Pikt is seen in resistance to proteolytic enzymes. According to Schlesinger et al. (39), ubiquitin has a marked resistance to the proteolytic enzymes used in the present study. In contrast, Pikt was completely hydrolyzed by protease XIV and partially hydrolyzed by pepsin.
Thus, Pikt appears to be a ubiquitin-like peptide that has antimicrobial activity. Ubiquitin-like peptides from the fruiting bodies of edible mushrooms, including Pleurotus sajor-caju, Pleurotus ostreatus, and Cantharellus cibarius, have been characterized so far (29, 47, 48). These peptides show an N-terminal sequence identical to that of ubiquitin, and all have RNase- and translation-inhibiting activities. Studies are in progress to determine whether Pikt exhibits similar activities.

FOOTNOTES
* Corresponding author. Mailing address: Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agroalimentari, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy. Phone: 39-079-229314. Fax: 39-079-229370. E-mail:
i.mannazzu{at}uniss.it 
Published ahead of print on 29 December 2008. 

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Applied and Environmental Microbiology, February 2009, p. 1129-1134, Vol. 75, No. 4
0099-2240/09/$08.00+0 doi:10.1128/AEM.01837-08
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