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Clinical and Vaccine Immunology, October 2006, p. 1155-1161, Vol. 13, No. 10
1071-412X/06/$08.00+0 doi:10.1128/CVI.00058-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Comparison of the Proteosomes and Antigenicities of Secreted and Cellular Proteins Produced by Mycobacterium paratuberculosis
Donghee Cho and
Michael T. Collins*
Department of Pathobiological Sciences, School of Veterinary Medicine, University of WisconsinMadison, 2015 Linden Drive, Madison, Wisconsin 53706
Received 14 February 2006/
Returned for modification 14 April 2006/
Accepted 12 July 2006

ABSTRACT
The protein expression profiles and antigenicities of both culture
filtrates (CF) and cellular extracts (CE) of
Mycobacterium paratuberculosis were compared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis
(SDS-PAGE), one-dimensional electrophoresis (1-DE) and 2-DE
immunoblotting, and enzyme-linked immunosorbent assay (ELISA).
The CF proteins were harvested from supernatants of stationary-phase
liquid cultures and concentrated by size exclusion filtration.
The CE proteins were extracted by mechanical disruption of cells
using glass beads and a high-speed agitator. Analysis of SDS-PAGE
gels showed that the majority of CF proteins had low molecular
masses (<50 kDa), whereas CE protein mass ranged more evenly
over a broader range up to 100 kDa. By 2-DE, CF proteins had
a narrow array of pI values, with most being between pH 4.0
and 5.5; CE proteins spanned pI values from pH 4.0 to 7.0. The
antigenicities of CF and CE proteins were first determined by
1-DE and 2-DE immunoblotting with serum from a cow naturally
infected with
M. paratuberculosis. The serum reacted strongly
to more proteins in the CF than the CE. Sera from 444 infected
and 412 uninfected cattle were tested by ELISA with CF and CE
as solid-phase antigens. Receiver-operator characteristic curve
analysis of the ELISA results showed a significantly greater
area under the curve for CF compared to CE (
P < 0.05). A
high degree of variability in protein binding patterns was shown
with 1-DE immunoblot analysis with 31 sera from
M. paratuberculosis-infected
cattle. Collectively, these results indicate that serologic
tests for bovine paratuberculosis may be improved by using proteins
derived from CF instead of CE. To maximize the diagnostic sensitivity
of serologic tests, multiple proteins will be required. Even
so, a CF ELISA may not be able to detect all
M. paratuberculosis-infected
cattle, in particular those in the early stages of infection
that have yet to mount an antibody response.

INTRODUCTION
Bovine paratuberculosis is diagnosed either by detecting the
causative agent
Mycobacterium paratuberculosis (also known as
Mycobacterium avium subsp.
paratuberculosis) or an immune response
to the agent (
6). Microbiological culture of the organism from
feces is a widely used diagnostic test and is considered the
reference assay against which other tests are compared. Culture
of
M. paratuberculosis on conventional solid bacteriological
media is laborious and slow, requiring up to 16 weeks for assay
completion (
6). Detection of a cellular immune response by either
skin testing or stimulation of leukocytes for gamma interferon
release is useful for earlier diagnosis of infection, but these
assays suffer from high variability and lower specificity (
11,
16,
17,
20). Serologic assays, such as enzyme-linked immunosorbent
assays (ELISAs), have low diagnostic sensitivity during early
phases of the infection but are a useful tool for Johne's disease
control because of low-cost, high-throughput, standardized protocols
and correlation with
M. paratuberculosis fecal-shedding levels.
A recent comparison of commercial ELISA kits for bovine paratuberculosis
diagnosis illustrated that the assays performed comparably overall,
with diagnostic sensitivity ranging from 27.9 to 44.5% for fecal
culture-positive cattle (
8). Interestingly, numerous individual
cattle were strongly responsive in one assay and not another
(
8). Although exact details of the antigen preparation methods
for commercially available ELISA kits are proprietary, either
protoplasmic fractions, other cellular extracts, or lipoarabinomannan
are likely the basis of most assays because of the higher antigen
yields and ease of preparation (
1,
4,
7,
9,
21,
34,
37,
46).
Based on a literature review, proteins secreted from
M. paratuberculosis into the extracellular environment have received little attention
as serodiagnostic assay antigen candidates (
21). In contrast,
secreted proteins of
Mycobacterium tuberculosis are the focus
of considerable research as human medicine tries to improve
diagnostic assays for tuberculosis (
18,
22).
In previous work, we observed that culture conditions significantly influence protein expression profiles of M. paratuberculosis (39). The purpose of the present study was to compare the M. paratuberculosis protein antigens found in the cellular to extracellular compartments by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), immunoblotting, and ELISA. This work forms the basis of a search for secreted proteins that may improve serodiagnostic tests for bovine paratuberculosis.

MATERIALS AND METHODS
Bacterial strains.
M. paratuberculosis JTC303 was propagated in Middlebrook 7H9
(7H9) broth (Becton Dickinson, Cockeysville, MD) and modified
Watson-Reid (WR) broth supplemented with mycobactin J (Allied
Monitor, Fayetteville, MO). In addition, 7H9 broth was supplemented
with 10% oleic acid-albumin-dextrose-catalase (Becton Dickinson).
WR broth (pH 6.0) was prepared without the addition of sodium
pyruvate (
44).
Mycobacterium phlei (ATCC 11758) was cultivated
in WR broth, and cellular protein extracts were used to absorb
cross-reacting serum antibodies prior to immunoblotting (preabsorption).
Cellular extracts and culture filtrates were harvested when
growth had reached stationary phase (
38).
Culture filtrates (CF).
Bacterial cells grown in WR broth were removed by centrifugation at 30,000 x g for 10 min, followed by filtration (0.2-µm pore size; Nalge Nunc, Rochester, NY). The filtrate was then concentrated roughly 100-fold by using Centricon Plus-80 (Millipore, Billerica, MA) and dialyzed in 10 mM phosphate-buffered saline (PBS; pH 6.8). The concentration of soluble CF proteins was determined by the BCA protein assay kit (Pierce, Rockford, IL).
Cellular extracts (CE).
M. phlei and M. paratuberculosis were grown in WR or 7H9 broth, harvested by centrifugation (30,000 x g for 10 min), and washed three times in 10 mM PBS (pH 6.8). The resultant cell pellets were then homogenized by using an overhead stirrer (Wheaton Instruments, Milville, NJ) for 3 min on ice to minimize clumping of cells. After the addition of a protease inhibitor cocktail (Complete, Mini, EDTA-free, 0.05% [vol/vol]; Roche Diagnostics GmbH, Germany), 10 ml of the homogenized cell pellets was mixed with 20 g of glass beads (0.10 to 0.11 mm; Glassperlen; B. Braun Biotech International GmbH, Germany). The mixture was vigorously agitated for 10 min, while cooling with liquid CO2, using a high-speed agitator (model MSK; Braun Instruments, Allentown, PA). The homogenate was then centrifuged at 30,000 x g for 30 min, and the CE proteins were stored at 70°C. The concentration of CE proteins was also determined by using a BCA protein assay kit (Pierce, Rockford, IL).
Sera.
Sera were collected from healthy uninfected dairy cattle resident in herds at status level 4 in the U.S. Voluntary Bovine Johne's Disease Herd Status Program (8). Sera from cattle known to be infected with M. paratuberculosis were collected from cows in eight different dairy herds. All were naturally infected, clinically normal, and fecal culture positive (8). One of the infected cattle, Dolly, was euthanized according to AALAC protocols to verify her disseminated M. paratuberculosis infection by histopathology and culture of tissues. Serum sufficient to complete the one- and two-dimensional electrophoresis (1-DE and 2-DE) immunoblot analyses was obtained from this cow (i.e., the positive control).
Serum absorption.
Most ELISA kits for paratuberculosis diagnosis enhance assay specificity by absorbing clinical sample sera with antigens derived from M. phlei (9, 25, 46). The importance of this absorption step was well described by Bech-Nielsen et al. These authors reported that the sensitivity of an ELISA without absorption was 0% at 100% specificity in a subclinically infected herd, with absorption sensitivity increased to 33.3% (1). This procedure was adapted for immunoblot analysis and used in the present study to evaluate antigen specificity. The absorbent was a CE that had been prepared from an early-stationary-phase culture of M. phlei grown in WR broth. A similarly prepared CE of M. paratuberculosis served as an absorption control. Absorption with CF proteins was not possible due to low CF protein yield (approximately 68 mg from 1 liter of WR media). Serum absorption was performed by mixing sera with 1,500 µg of CE proteins/ml, followed by incubation at room temperature for 30 min.
1-DE.
The CE and CF proteins were separated under reducing conditions as described by Xiong et al. (45) with commercial precast gels (Jule Biotechnologies, Milford, CT). Gels were prepared in Tris buffer containing SDS (0.375 M Tris-HCl [pH 8.8], 0.1% SDS). Protein samples (10 µg) were loaded into each gradient gel (10 to 20% polyacrylamide, 10 wells, 1.5-mm thickness) well after gel placement in the electrophoresis apparatus (Bio-Rad Mini Protein II; Bio-Rad, Hercules, CA). Gels were electrophoresed for 2 h at 150 V, and the protein bands were visualized by Coomassie brilliant blue staining.
2-DE.
Proteins were mixed with 2-DE sample buffer (0.3% [wt/vol] SDS, 200 mM dithiothreitol, 28 mM Tris-HCl, 22 mM Tris base). After boiling for 10 min in a water bath, the mixture was placed on ice for 10 min. Nuclease-containing cleaning buffer (24 mM Tris base, 476 mM Tris-HCl, 50 mM MgCl2, 500 Kunitz units of DNase I/ml, 2.5 mg of RNase A/ml) was added to the sample buffer at a 1:10 ratio, followed by mixing by pipetting, and placed on ice for 10 min. Rehydration buffer (8.0 M urea, 2% CHAPS {3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate}, trace amounts of bromophenol blue, 2.8 mg of dithiothreitol/ml, and 0.5% [vol/vol] commercial IPG buffer) was then added to the sample and cleaning buffer at 4:1 ratio. Electrophoresis was performed by using an IPGphore isoelectric focusing system (Amersham Bioscience, Uppsala, Sweden) with a pH 4 to 7 nonlinear IPG DryStrip (Amersham Bioscience). The program was set to run 12 h for rehydration, 500 V · h at 500 V, 1,000 V · h at 1,000 V, and 50,000 V · h at 8,000 V. Each IPG strip was loaded with 100 µg of soluble protein. Isoelectric focused strip gels were then placed into equilibration buffer (50 mM Tris-Cl, 6 M urea, 30% glycerol, 2% SDS, trace amounts of bromophenol blue, and double-distilled water) for 20 min. The equilibrated strips were loaded onto precast 2-DE gels with exponential gradients of 10 to 20% (wt/vol) acrylamide (Jule, Inc., Milford, CT). Protein spots were stained with Brilliant Blue R (Sigma, St. Louis, MO) or transferred to a nitrocellulose membrane (0.2-µm pore size; Bio-Rad) for immunoblotting.
Immunoblotting.
Protein transfer from acrylamide gels to nitrocellulose membranes (0.2-µm pore size; Bio-Rad) was performed as described by Davies et al. using Tris-glycine buffer containing 0.0375% SDS and 20% methanol (10). Before reaction with serum, nitrocellulose membranes were incubated for 1 h in blocking buffer (1% bovine serum albumin in PBS-0.1% Tween). Reaction of proteins with antibodies in either absorbed or nonabsorbed sera was performed for 15 h at room temperature on a rocking platform. Horseradish peroxidase (HRP)-conjugated secondary antibody to bovine immunoglobulin G (IgG; Bethyl, Montgomery, TX) was then added to the membrane, and blots were developed with 3,3'-diaminobenzidine tetrahydrochloride (Sigma, St. Louis, MO) in Tris-buffered saline (pH 7.6).
Documentation and image analysis.
Digital images of each gel were made by using a high-resolution scanner equipped with a transparency unit (PowerLook III; UMAX Technologies, Inc., Dallas, TX). Image analysis of 2-DE immunoblot paper was performed by using computer software (Phoretix 2D Advanced, version 6.01; Nonlinear Dynamics, Durham, NC). The net intensity of each spot was obtained after subtraction of the background. For 1-DE immunoblots, the band location and intensity were measured by using image analysis software (1D image analysis software; Kodak, NY).
ELISA and data analysis.
The CE or CF proteins were diluted in coating buffer (KPL, Gaithersburg, MD) to a final concentration of 1 µg/ml, and 100 µl of each antigen was coated onto 96-well plates (Maxisorp; Nalge Nunc International, Rochester, NY) at 4°C overnight. After being washed, the wells were blocked by adding 10% bovine serum albumin (KPL) at 37°C overnight. Absorbed serum was added to each well, followed by incubation for 30 min at room temperature. Wells were then washed three times with washing buffer (KPL). Antibody binding was detected by using HRP-conjugated secondary antibody to bovine IgG (Bethyl) and TMB substrate (TMBE-500, Moss, Inc., Pasadena, MD). The optical density (OD) of the final reaction in each well was measured at 450 nm (µQuant; Bio-Tek instruments, Inc., Winooski, VT). Receiver-operator characteristic curves were generated, and the area under each curve was determined and compared by using Prism version 4.0 (GraphPad Software, Inc.) (14). The difference between mean ODs for the two antigen preparations, CF and CE, was evaluated by using the Wilcoxon signed-rank test.

RESULTS
Antigenicity analysis and immunoblot by 1-DE.
The CE protein profiles obtained differed depending on which
culture medium was used to grow
M. paratuberculosis (WR versus
7H9) as reported previously (
38). Even greater variability was
seen between the SDS-PAGE protein profiles for the two fractions,
CF and CE (Fig.
1). Immunoblots further highlighted the antigenic
disparity between CE and CF proteins (Fig.
2). Weak staining
and few bands appeared after immunoblotting for CE proteins
produced from
M. paratuberculosis grown in WR or 7H9 medium.
This pattern was observed both before and after
M. phlei absorption
(Fig.
2A and B, lanes 1 and 2). In contrast, immunoblot bands
were more numerous and more intensely stained using CF proteins
(Fig.
2A and B, lane 3). Low molecular mass proteins (<26
kDa) showed particularly strong reactivity with the positive
control serum (Dolly). Minimal changes to this immunoblot pattern
were seen when the serum was absorbed with
M. phlei antigens
(Fig.
2A, lane 3, versus panel B, lane 3).
Proteome and immunoblot analysis by 2-DE.
Image analysis of 23-by-30-cm 2-DE gels resolved approximately
400 (CE) and 240 (CF) proteins (Fig.
3). The CE proteins were
evenly distributed by mass and pI on the 2-DE gel. In contrast,
most CF proteins were <37 kDa and had acidic pI values (pH
4 to pH 5.5). Several proteins in both CE and CF preparations
appeared as strings of spots of similar masses but different
pIs, suggesting the existence of proteins modified by phosphorylation,
glycosylation, or acylation (Fig.
3). The 2-DE immunoblots of
CE and CF preparations were done with or without
M. phlei CE
protein serum absorption (Fig.
4A). The total staining intensity
of all proteins was determined and compared by image analysis
software (Fig.
4B). The total immunoreactivity of serum from
an
M. paratuberculosis-infected cow was greater with CF than
CE proteins, a finding in agreement with the 1-DE immunoblot
results (Fig.
2). The number of immunoreactive spots after serum
absorption was much lower for both CE and CF antigens, but the
effect was greater for CE proteins than for CF proteins. Some
CF proteins' immunoblot staining intensity was not affected
by serum absorption.
Antigenicity comparisons by 1-DE immunoblotting with multiple sera.
The antigenicities of CE and CF proteins by 1-DE immunoblot
analysis were compared by using six sera randomly chosen from
the population of >400 sera from
M. paratuberculosis-infected
cattle. Using image analysis software, each band's location
was identified, and its net intensity was calculated. The total
staining intensity of all bands was compared as the relative
net intensity (Fig.
5). Although some sera had weak antibody
responses to CE and CF, the signals to CF were in general much
stronger.
Comparison of CF and CE by ELISA.
Sera from 444 infected and 412 infection-free cattle were tested
by ELISA with CE and CF proteins as the solid-phase antigen.
The mean ELISA OD values for CE and CF antigens were significantly
different (
P < 0.0169 and
P < 0.001) for infected and
infection-free cattle, respectively (Fig.
6). Receiver-operator
characteristic analysis showing the relationship between specificity
and sensitivity revealed that the area under each curve was
significantly greater for CF than for CE antigens (0.7716 and
0.6623, respectively;
P < 0.05).
Variability of immunoblot patterns to CF proteins.
Immunoblot analyses with sera from 31
M. paratuberculosis-infected
cattle and 6 infection-free cattle were done after first absorbing
sera with
M. phlei cellular extract proteins. Among the sera
from infected cattle, protein binding patterns were highly variable
(Fig.
7A). Seventeen cattle showed strong serum antibody binding
to CF proteins of approximately 10, 15, 23, 30, 35, and 50 kDa,
but no single protein was reactive with the serum antibody from
all 17 cattle. The protein binding patterns for sera from the
other 14
M. paratuberculosis-infected cattle were the same as
for the sera from uninfected cattle. Sera from uninfected cows,
after absorption with
M. phlei CE proteins, showed weak reactions
to a 25-kDa band of
M. paratuberculosis CF. This weak reaction
also was seen after absorption of sera with
M. paratuberculosis CE proteins (Fig.
7B).

DISCUSSION
The proteome of
M. paratuberculosis strain JTC303 CF was different
from that of the CE. Specifically, CF proteins generally had
lower pIs (4.4 to 5.5) and smaller masses (most <30 kDa)
than CE proteins. A similar protein pattern was shown in CF
prepared from
M. paratuberculosis strain ATCC 19698 cultured
in Sauton media, suggesting that this difference is not caused
by the strains of organism or culture medium (
30). Rosseels
et al. also showed by SDS-PAGE that
M. paratuberculosis CF was
markedly different from
M. tuberculosis H37Rv CF, where major
protein bands were visible at up to 100 kDa. Other mycobacteria
also have been shown to have proteins with more acidic pI values
than CE proteins (
5,
19,
24). In work with
Escherichia coli,
Helicobacter pylori, and
M. tuberculosis, researchers have suggested
there is a correlation between pI and subcellular protein localization,
especially for cytoplasmic and integral membrane proteins (
33,
41). Cytoplasmic proteins have pIs in the range of 5 to 6, whereas
integral membrane proteins have pIs of 8.5 to 9. The data presented
by Pleissner et al. also revealed a distinct bimodal protein
pI pattern centered at around 5 and 9 for
M. tuberculosis proteins
(
29). We suspect that the correlation of a protein's pI with
subcellular localization extends to secreted proteins. Moreover,
the narrow range of pIs we found in
M. paratuberculosis CF contrasted
with CE supports the idea that these proteins are actively secreted
and not simply released by autolysis of the cells as has been
previously proposed (
43).
The low pI value of CF proteins may point to their role in macrophage phagolyososome fusion. The low pH within lysosomes, i.e., pH 4.5 to 5.0, favors activation of a hydrolytic enzyme that degrades a wide range of macromolecule and microbes (13). In addition to being optimal for enzyme activation, this low pH would make many secreted mycobacterial proteins insoluble, with solubility being lowest when the pH approaches the pI of the protein. This fact may explain why pathogenic mycobacteria avoid fusion of the phagosome in which they reside in cells with lysosomes (31) and why they have mechanisms that modulate the pH inside the phagosome (36).
The immunoblot and ELISA results presented here showed that serum antibodies from naturally M. paratuberculosis-infected cattle react more strongly and to more proteins in CF than in CE. The obvious explanation for this difference is accessibility. Secreted proteins are more available for interaction with antigen-presenting cells, and T and B lymphocytes, which lead to antibody production. The accessibility of the immune system to most CE proteins, except for those on the mycobacterial cell surface, is likely to be limited.
The diversity of binding patterns of bovine serum antibodies to CF proteins observed in the present study is consistent with that reported for other mycobacterial infections in cattle, deer, and humans (23, 42). Beck et al. found at least four serum antibody response profiles when testing human tuberculosis patient sera against M. tuberculosis antigens (2, 3). Serum antibody responses are primarily affected by the stage of infection. Little or no detectable antibody is produced until the Th1 to Th2 immune response shift occurs (28). The same pattern is seen in paratuberculosis: the early cell-mediated immune response contains the infection for most of the natural history of the M. paratuberculosis infection. The organism appears to be in a dormant state during this stage of infection. When, for unknown reasons, the animal's immune system loses control of the pathogen, or the pathogen begins active replication, the organism disseminates, and the host response shifts to a Th2 type immune reaction. The hallmark of this infection stage is production of detectable serum antibodies. A positive relationship has been shown between the level of serum antibody production and the number of M. paratuberculosis isolated from fecal samples (8, 27).
A second possible explanation for the diversity in antibody-antigen binding patterns is host response variability to the infection. Paratuberculosis has diverse histopathological forms paralleling those of leprosy, ranging from lepromatous (multibacillary) to tuberculoid-like (paucibacillary) with many intermediate lesion categories (15). All forms are thought to represent the advanced stages of disease resulting from infection early in life since adult animals are generally resistant to infection (28). Tanaka et al. showed that cytokine gene expression profiles differ in lepromatous versus tuberculoid forms of paratuberculosis (40). Lepromatous lesions are associated with strong Th2-type cytokine expression and a strong antibody response.
Hormonal, physiological, nutritional, and pharmaceutical influences on the host immune response, both direct and indirect, may also contribute to serum antibody binding differences seen during paratuberculosis in cattle. During the few weeks prior to and after parturition, serum levels of antibody to M. paratuberculosis drop precipitously as antibody is shunted from serum into the colostrum (35). Feola et al. demonstrated the effects of bovine growth hormone on M. paratuberculosis growth rates both inside and outside bovine macrophages (12). Levamisol-treated cattle showed enhanced cell-mediated immune responses to M. paratuberculosis (26). Other parasiticides and corticosteroids also may have immunomodulatory effects that could influence the character of serum antibody production to this pathogen (32).
Our study has several important implications for the serodiagnosis of bovine paratuberculosis. First, serologic tests may be improved by the use of M. paratuberculosis proteins derived from CF instead of CE. Second, to increase the serodiagnostic sensitivity for M. paratuberculosis infection, multiple antigens are likely required. Finally, depending on the stage of infection, not all fecal-culture-positive cows may have detectable serum antibodies to any M. paratuberculosis protein.

ACKNOWLEDGMENTS
We thank Elizabeth Manning, Alice Yuroff, and Sung Jae Shin,
Department of Pathobiological Sciences, University of WisconsinMadison,
for valuable comments and critical review of the manuscript.
This research was funded in part by the USDA-NRI Competitive Grant Program (project WIS 04405).

FOOTNOTES
* Corresponding author. Mailing address: Department of Pathobiological Sciences, School of Veterinary Medicine, University of WisconsinMadison, 2015 Linden Drive, Madison, WI 53706. Phone: (608) 262-8457. Fax: (608) 265-6463. E-mail:
mcollin5{at}wisc.edu.


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Clinical and Vaccine Immunology, October 2006, p. 1155-1161, Vol. 13, No. 10
1071-412X/06/$08.00+0 doi:10.1128/CVI.00058-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
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