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Infection and Immunity, December 2000, p. 6685-6690, Vol. 68, No. 12
0019-9567/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Multiple Mechanisms of Phase Variation of PorA in
Neisseria meningitidis
Arie
van der
Ende,*
Carla T. P.
Hopman, and
Jacob
Dankert
Department of Medical Microbiology, Academic
Medical Center, University of Amsterdam, and Reference Laboratory for
Bacterial Meningitis, University of Amsterdam/RIVM, 1100 DE Amsterdam,
The Netherlands
Received 6 July 2000/Returned for modification 14 August
2000/Accepted 25 September 2000
 |
ABSTRACT |
Previously, we reported that PorA expression in Neisseria
meningitidis is modulated by variation in the length of the
homopolymeric tract of guanidine residues between the
35 and
10
regions of the promoter or by deletion of porA. To reveal
additional mechanisms of variation in PorA expression, the
meningococcal isolates from 41 patients and 19 carriers were studied.
In addition, at least 3 meningococcal isolates from different body
parts of each of 11 patients were analyzed. Sequence analysis of the
porA promoter showed that the spacer between the
35 and
10 regions varies in length between 14 and 24 bp. PorA expression was
observed in strains with a porA promoter spacer of 16 to 24 bp. All but one strain with a porA promoter spacer of 16 to
20 bp and undetectable PorA expression have a homopolymeric tract of 8 or 6 instead of 7 adenine residues in the porA coding
region. The other PorA-negative strain had a single-base-pair deletion
in the coding region. The highest level of PorA expression was observed
in strains with a promoter spacer of 17 or 18 bp. PorA expression was
reduced twofold in strains with a porA promoter spacer of
16 or 19 bp. Strains with a 16-bp promoter spacer with substitutions in
the polyguanidine tract displayed increased levels of PorA expression compared to strains with a homopolymeric tract of guanidine residues in
the porA promoter. In conclusion, meningococci display
multiple mechanisms for varying PorA expression.
 |
INTRODUCTION |
Major outer membrane proteins of
Neisseria meningitidis are of interest, since their
antigenic variation is used for serological discrimination between
isolates (1, 7). In addition, meningococcal outer membrane
vesicles containing major outer membrane proteins are under
investigation as experimental vaccines to prevent meningococcal disease
(8, 12). Class 1 protein, or PorA, is of particular interest, since monoclonal antibodies directed against
serosubtype-specific epitopes on PorA proved to exert bactericidal
activity in serum and confer protection against N. meningitidis infection in an animal model (27, 28). In
clinical trials with meningococcal outer membrane-based vaccines, the
induced bactericidal activity in serum was predominantly attributed to
the presence of antibodies directed against PorA (4, 22).
Since PorA is exposed to antigenic variation, the newer PorA-based
vaccines contain multiple antigenic variants of PorA (5,
35). Field trials with a hexavalent PorA-based vaccine have
already been performed (24).
PorA can be expressed by most clinical isolates, but its levels of
expression vary considerably (13, 33, 34). Since stable
expression of PorA in meningococci during infection is a prerequisite
for the PorA vaccine to be effective, knowledge of the genetic
mechanism of the variable PorA expression is important. Recently,
isolates from patients with meningococcal disease with the complete
porA gene deleted have been described (34).
Previously, we reported PorA phase variation at the transcriptional
level, mediated by a variable homopolymeric tract of guanidine residues between the
35 and
10 domains of the porA promoter
(33). For this report we studied additional mechanisms of
PorA expression variation and porA promoter sequences among
meningococcal isolates from 52 patients with meningococcal disease and
19 N. meningitidis carriers. From 11 of the 52 patients with
meningococcal disease, three isolates, cultured from different sites
and specimens, were studied.
 |
MATERIALS AND METHODS |
Strains and culture conditions.
From the collection of the
Reference Laboratory for Bacterial Meningitis, University of Amsterdam,
Amsterdam, The Netherlands, and Rijksinstituut voor Volkgezonheid en
Milieu, Bilthoven, The Netherlands, 66 strains from 41 patients with
meningococcal disease and 19 healthy carriers were selected (see Table
1). These 66 strains represent all 29 lineages present in the
collection of the Reference Laboratory, including reference strains for
serogrouping. A second group of isolates cultured from 11 patients was
studied (see Table 2). Three isolates per patient were taken from
different sites and specimens. All isolates were stored at
70°C
within four passages.
From the frozen stock culture of each isolate, bacteria were grown on a
chocolate agar plate (3% hemoglobin in GC agar base) (Oxoid CM 367;
Unipath, Basingstoke, England) at 37°C in a humidified atmosphere of
5% CO2 in air for 18 h. One colony was selected from
the culture plate and resuspended in 100 µl of deionized H2O. A loop of this suspension was subcultured on a
chocolate agar plate. Part of this culture was stored at
70°C, and
another part was used to inoculate 200 ml of tryptic soy broth (Difco Laboratories, Inc., Detroit, Mich.) for the preparation of the outer
membrane protein fraction. The remaining suspension in deionized H2O was heated at 100°C for 10 min. After centrifugation
for 2 min in an Eppendorf centrifuge at maximum speed, 10 µl of the supernatant was used in a PCR to amplify the porA promoter region.
Fluorescence-based sequencing and analysis.
The
porA promoter region was amplified using primers PorA5
(34) and P21Rev (5'-ACGGCCGGCTTTGATTTCGCCGTACAG-3')
or PorA72 (5'-GCACGAGGTCTGCGCTTGAATTG-3') and P21Rev.
The DNA sequences of both strands of these amplicons, of 330 and 295 bp, respectively, were determined by a PCR-based sequence reaction with
fluorescent dye-labeled dideoxynucleotide terminators using AmpliTaq
DNA polymerase FS (Perkin-Elmer, Gouda, The Netherlands) and primers
PorA5 and P21Rev or PorA72 and P21Rev according to the instructions
supplied by Applied Biosystems Incorporated (Foster City, Calif.). The sequences were analyzed on an automatic sequenator (model 373-stretch; Applied Biosystems Incorporated).
PorA expression quantification.
Outer membrane proteins were
isolated and analyzed with sodium dodecyl sulfate-polyacrylamide gel
electrophoresis as described by Poolman et al. (25). Ten
micrograms of the outer membrane protein fraction of each isolate was
loaded on a sodium dodecyl sulfate-11% polyacrylamide gel. After
staining with 0.1% Coomassie brilliant blue R (Sigma, St. Louis, Mo.)
in acetic acid-methanol (10%/25% in H2O) and destaining,
protein patterns were visualized and an image was captured with a video
camera. Analysis of the images was performed using Gelcompar software
3.1 (Applied Maths, Kortrijk, Belgium). The amount of PorA in each
strain was expressed as the percentage (1% = 1 arbitrary unit) of the
total amount of outer membrane protein of the strain visible in the gel.
Western and colony immunoblotting.
PorA was identified by
Western immunoblotting (32) using PorA-specific monoclonal
antibodies (1). For colony blotting, colonies were
transferred to nitrocellulose (pore size, 0.45 µm; Schleicher & Schluell, Dassel, Germany) and immunologically stained as described
previously (13).
Statistics.
Significance of differences was calculated by
the chi-square test (Yates corrected) and the two-tailed Fischer exact test.
 |
RESULTS |
PorA phase variation by length variation of a homopolymeric adenine
tract in the porA coding region.
First, 66 strains
from 41 patients with meningococcal disease and 19 healthy carriers
were studied (Table 1). The number of
base pairs forming the spacer between the
35 and
10 domains of the
porA promoter ranged from 14 to 24. PorA expression was observed in strains with a porA promoter spacer of 16 to 24 bp (Fig. 1; Table 1).
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TABLE 1.
Serogroup, source, porA promoter spacer length
and composition, and PorA expression of meningococcal isolates
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FIG. 1.
Outer membrane profiles of meningococci with different
porA promoter spacer sequences. Strains YP1 and YP2 are from
one carrier; strains 860183-I and 860183-II are the CSF and blood
isolates from one patient.
|
|
Surprisingly, PorA expression was undetectable in four of the strains
with a porA promoter spacer of 16 to 20 bp (Table 1; Fig. 1
and 2B). Strain 800377, with a
porA promoter spacer of 17 bp, appeared to have a deletion
of a single bp at position 39 (from the start codon) in the
porA reading frame (Fig. 2B). Predicted translations of
porA reveal that this deletion introduces a frame shift,
which truncates the coding sequence at codon position 40. In strain
851267, with a porA promoter spacer of 20 bp, a 7-bp
homopolymeric tract of adenine residues close behind the start codon
was extended with 1 bp, also resulting in a frame shift. The primary
culture plate YP of the throat swab of one carrier contained 91%
PorA-positive and 9% PorA-negative expression variants as identified
by colony immunoblotting. One PorA-negative expression variant (YP1)
and a positive PorA expression variant (YP2) were selected for further
analysis (Fig. 2B). The porA promoter spacer was 16 bp long,
but the homopolyadenine tract in the porA coding region in
these variants was 8 bp (strain YP1) and 7 bp (strain YP2) long,
respectively. In addition, from the culture plate of strain YP1, a
PorA-positive variant, which was present with a frequency of
10
3, was selected which had a polyadenine tract of 7 bp
(not shown). Furthermore, the cerebrospinal fluid (CSF) isolate
860183-I, with a porA promoter spacer of 17 bp and a
polyadenine tract in the porA coding region of 7 bp,
displayed strong PorA expression, while the isogenic blood isolate
860183-II (from the same patient) with a polyadenine tract of 6 bp had
undetectable PorA expression levels (Fig. 1 and 2B). In addition, the
blood isolate contained variants in which the porA gene was
completely deleted, as described previously (34).

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FIG. 2.
(A) Sequence variation in the promoter region of the
outer membrane protein PorA among 66 strains of N. meningitidis. The putative 35 and 10 domains are underlined.
Polymorphisms in the porA promoter spacer are in boldface.
(B) Association between PorA expression and variation in the
homopolymeric tract of adenine residues and a nonsense mutation in the
porA coding region. The start codon of each sequence is in
boldface.
|
|
Predicted translations of porA show that full coding
integrity is maintained with a repeat of seven adenine residues, while expansion or reduction by one residue introduces a frame shift, which
truncates the coding sequence.
PorA expression associated with the length and composition of the
spacer between the
35 and
10 domains of its promoter.
The
porA promoter contained a variable homopolymeric tract of 8 to 18 guanidine residues in the spacer between the putative
35 and
10 domains (Fig. 2A). Nine strains had one or more mutations in the
porA promoter spacer, replacing one or two of the residues in the homopolymeric tract of guanidine residues with a thymidine or
adenine (Fig. 2). In addition, for isolate 980218 and isolates YP1 and
YP2, the homopolymeric tract of thymidine residues was extended by 1 or
2 bp, respectively, compensated for by a reduction of an equal number
of base pairs of the interrupted polyguanidine tract.
PorA expression of the strains ranged widely (Fig. 1 and
3). The PorA expression was strongest in
33 strains with a spacer region of 17 or 18 bp (Fig. 3). The PorA
expression level of the majority of strains with promoter spacer
regions of 16 and 19 bp was significantly lower. The average PorA
expression level in 6 strains with a mutated porA promoter
spacer of 16 bp was 1.6 times higher than that of the strains with a
corresponding porA promoter spacer with a homopolymeric
tract of guanidine residues, although this difference did not reach a
significant level (Fig. 3). Expression of PorA was undetectable in
strains with a promoter spacer region shorter than 16 bp (Fig. 1 and
3). The PorA expression of the 7 strains with a polyguanidine tract in
the porA promoter spacer length of
21 bp was only weak or
not detectable. For those 4 strains with a weak PorA expression level
and of subtypes for which a monoclonal antibody was available, Western
immunoblotting also showed a low level of PorA expression.

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FIG. 3.
Association between the mean PorA expression levels and
the length of the porA promoter spacer region with a
contiguous polyguanidine tract ( ) or with an interrupted
polyguanidine tract ( ). The whiskers indicate the standard errors of
means. The amount of PorA is expressed as a percentage of the outer
membrane protein fraction. Isolates with a mutation in the
porA coding region were excluded. ns, not significant.
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|
PorA expression of meningococcal isolates from different specimens
of a single patient.
The distributions of the porA
promoter spacer lengths among isolates from carriers and among isolates
from patients were different. The isolates from 8 of the 19 (42%)
carriers had a promoter spacer of less than 17 bp, but the isolates
from only 3 of the 41 (7%) patients had such a low number of base
pairs in the porA promoter spacer (P < 0.05). These results might indicate that the porA promoter spacers of carrier isolates were shorter than those of patient
isolates. Therefore, three isolates from different sites and specimens
from 11 patients were analyzed for their PorA expression, porA promoter spacer sequence, and homopolymeric adenine
tract in the porA coding region (Table
2). The multiple meningococcal isolates
from different specimens from the same patient had identical porA promoter sequences, except for patient 901168. The
throat isolate had a porA promoter spacer of 18 bp and high
PorA expression, while the isolates from blood and CSF had a
porA promoter spacer of 16 bp and low PorA expression. The
PorA expression in the isolates from the skin biopsy specimen, CSF, and
blood of patient 930470 was negative, due to a homopolymeric adenine
tract of 6 bp instead of 7 bp in the porA coding region.
 |
DISCUSSION |
It was reported earlier that the spacer between the putative
35
and
10 domains of the porA promoter varies in length due to a variable homopolymeric tract of guanidine residues in this spacer
(2, 29, 33). Meningococcal isolates with the porA gene deleted have been described (34). In addition,
meningococcal isolates with PorA expression levels that were not
anticipated based on their promoter sequence were recently encountered.
To reveal additional mechanisms of PorA expression variation, the meningococcal isolates from 41 patients and 19 carriers were studied.
The porA promoter spacer ranged from 14 to 24 bp in length
due to variation in the length of the homopolymeric guanidine tract. In
addition, the homopolymeric tract of thymidine residues of the
porA promoter spacer may also vary. One strain was found in which the polythymidine tract was increased by one thymidine residue, and in the two variants (YP1 and YP2) from the primary culture plate of
a throat swab the polythymidine tract was increased by two thymidine residues.
Carrier isolates had shorter porA promoter sequences than
patient isolates. However, the mean PorA expression levels of the isolates with a porA promoter spacer of <17 bp were higher
in carrier isolates than in isolates from patients, due to mutations in
the polyguanidine tract in four out of seven carrier isolates with a
porA promoter spacer of 16 bp. In addition, PorA expression did not differ among meningococci isolated from different sites of the
body, indicating that the level of PorA expression of meningococci at
different locations in the host had no selective advantage during
infection. However, porA-negative meningococci, which may appear after selection, being resistant to bactericidal antibodies against PorA were isolated from a patient's blood (34).
Although PorA expression was observed in strains with a promoter spacer
of 16 to 23 bp, the highest level of PorA expression was observed in
strains with a promoter spacer of 18 or 17 bp. These results are in
concordance with our earlier results (33) and with those
from Arhin and colleagues (2). The results are also
consistent with the recently published study of Sawaya and colleagues
(29). In their study, PorA expression gradually decreased when the length of the promoter spacer region was decreased from 18 to
16 bp by in vitro mutagenesis. However, in that study, porA promoters with spacers of >18 bp were not studied.
In Escherichia coli, the length of the promoter spacer
region is constrained to 17 ± 1 bp (10, 30). The data
from our study indicate that the length of the porA promoter
spacer in N. meningitidis might be less restricted. The
10
domain of the porA promoter is a complete match with the
consensus sequence of
10 domains of promoters in other prokaryotes,
while the putative
35 domain of the porA promoter is ill
defined. The putative
35 domain ATGGTT matches the
E. coli consensus
35 domain (TTGACA) only in
two out of six nucleotides (10). Absence of an identifiable
35 region or poor homology with the
35 consensus sequence may be
indicative of involvement of an auxiliary protein binding upstream of
the
10 domain and in this way substituting for the role of the
35
region (6). However, the sequence TGGTTT, which
is shifted 1 bp downstream compared to the ATGGTT sequence,
also has two matches with the consensus
35 sequence. The broad range of lengths of the porA promoter spacer region allowing PorA
expression may indicate that both
35 domains are being recognized by
RNA polymerase and may be used alternatively at the initiation of porA transcription.
An alternative explanation may be that the homopolymeric tract of
guanidine residues in the porA promoter adopts the A-helical structure instead of the B-helical conformation (6, 29, 36). The A-helical DNA structure has a shorter physical distance between base pairs as well as a decreased net twist compared to the B-helical DNA structure. In promoters with an A-helical structure, deletion of 1 bp from the optimal 17-bp spacer would have a greater impact on protein
expression than an insertion of 1 bp (6, 36). Our results
are consistent with this model. The average PorA expression levels of
strains with a porA promoter with a spacer of 16 bp is 1.9 times lower than that of strains that have a promoter with a spacer of
17 bp. Conversely, strains with a porA promoter spacer of 17 or 18 bp expressed similar amounts of PorA. In addition, PorA
expression is 1.6 times higher (although this difference is not
significant) in strains with a porA promoter with a 16-bp spacer containing an interrupted polyguanidine tract than in strains with a homopolymeric tract of guanidine residues in the porA
promoter, which is consistent with conversion of the A-helical DNA
structure into the B-helical DNA conformation of the porA
promoter spacer (6, 36).
In addition to the variation in PorA expression due to sequence
variation in the porA promoter region, PorA expression
variation may also be affected by other mechanisms. In our study,
porA expression also was altered due to extension or
shortening of a homopolymeric tract of adenine residues in the coding
region of porA of isogenic meningococcal strains. So the DNA
strand slippage mechanism causes PorA phase variation at the
transcriptional level and at the translational level. Phase variation
by the DNA strand slippage mechanism has been described for a variety
of microorganisms (11). Translational control by DNA
slipped-strand mispairing in Neisseria has been described
for the opacity proteins (18), lipopolysaccharide immunotypes (14), hemoglobin receptor HmbR (16,
26), capsular polysaccharide production (9), and
fimbrial expression (15) and seems to be a common mechanism
for varying the expression of genes that are important in the virulence
of pathogenic microorganisms.
PorA is the important component of group B meningococcal protein-based
vaccines, since capsule polysaccharides of group B meningococci are
poorly immunogenic. However, meningococci avoid the humoral host immune
response to this protein by antigenic variation (3, 17, 19, 20,
31) within PorA as well as by variation of its expression
(2, 13, 33). This study shows that PorA expression can be
varied in multiple ways. Slipped-strand mispairing during replication
in the homopolymeric tract of guanidine residues and/or thymidine
residues in the porA promoter as well as the homopolymeric
tract of adenine residues in the porA coding region yields
progenitors with a PorA expression different from that of their
parental bacterial cells. In addition, point mutations in the coding
region may result in meningococci without PorA expression. Also, PorA
expression may be absent due to deletion of the complete porA gene as previously described (34). In
addition, insertion of an IS element in the porA coding
region in isolates without PorA expression has also been observed
(23).
In summary, PorA expression can be varied by multiple mechanisms, which
in concert with antigenic variation of PorA might be indicative of a
limited efficacy of PorA-based vaccines.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Medical Microbiology, Academic Medical Center, University of Amsterdam, P.O. Box 22700, 1100 DE Amsterdam, The Netherlands. Phone: (31-20) 5664862. Fax: (31-20) 6979271. E-mail:
a.vanderende{at}amc.uva.nl.
Editor:
E. I. Tuomanen
 |
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Infection and Immunity, December 2000, p. 6685-6690, Vol. 68, No. 12
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Copyright © 2000, American Society for Microbiology. All rights reserved.
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