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Infect Immun, April 1998, p. 1622-1631, Vol. 66, No. 4
0019-9567/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
Copy Number of Pilus Gene Clusters in
Haemophilus influenzae and Variation in the hifE
Pilin Gene
Timothy D.
Read,
Sarah W.
Satola,
Jason A.
Opdyke, and
Monica M.
Farley*
Veterans Affairs Medical Center and
Department of Medicine, Emory University School of
Medicine, Decatur, Georgia 30033
Received 13 October 1997/Returned for modification 8 December
1997/Accepted 7 January 1998
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ABSTRACT |
Brazilian purpuric fever (BPF)-associated Haemophilus
influenzae biogroup aegyptius strain F3031 contains two identical
copies of a five gene cluster (hifA to hifE)
encoding pili similar to well-characterized Hif fimbriae of H. influenzae type b. HifE, the putative pilus tip adhesin of F3031,
shares only 40% amino acid sequence similarity with the same molecule
from type b strains, whereas the other four proteins have 75 to 95%
identity. To determine whether pilus cluster duplication and the
hifEF3031 allele were special features of
BPF-associated bacteria, we analyzed a collection of H. influenzae strains by PCR with hifA- and
hifE-specific oligonucleotides, by Southern hybridization
with a hifC gene probe, and by nucleotide sequencing. The
presence of two pilus clusters was limited to some H. influenzae biogroup aegyptius strains. The
hifEF3031 allele was limited to H. influenzae biogroup aegyptius. Two strains contained one copy of
hifEF3031 and one copy of a variant
hifE allele. We determined the nucleotide sequences of four
hifE genes from H. influenzae biogroup
aegyptius and H. influenzae capsule serotypes a and c. The
predicted proteins produced by these genes demonstrated only 35 to 70%
identity to the three published HifE proteins from nontypeable H. influenzae, serotype b, and BPF strains. The C-terminal third of
the molecules implicated in chaperone binding was the most highly
conserved region. Three conserved domains in the otherwise highly
variable N-terminal putative receptor-binding region of HifE were
similar to conserved portions in the N terminus of
Neisseria pilus adhesin PilC. We concluded that two pilus
clusters and hifEF3031 were not specific for
BPF-causing H. influenzae, and we also identified portions
of HifE possibly involved in binding mammalian cell receptors.
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INTRODUCTION |
Haemophilus influenzae is
a gram-negative bacterium that colonizes the human nasopharynx. Strains
with the serotype b capsule are highly virulent in nonimmune children,
whereas nonencapsulated (nontypeable H. influenzae [NTHI])
bacteria are an increasingly prevalent cause of localized respiratory
tract infections in the adult population. Many H. influenzae
strains express pili that enable the bacteria to agglutinate human
erythrocytes (9). The primary role of the pili is believed
to be initiation of contact between the bacterium and human cell during
infection. Analysis of the chromosomal region containing the pilus
determinants of H. influenzae serotype b (Hib) strains Eagan
and M43 revealed five genes, hifA to hifE,
necessary for pilus production (13, 16, 38, 40). The
H. influenzae genes have sequence homology with, and have
similarities in organization to, the Pap and type I pilus genes
(8, 9, 37). HifA is the major pilus antigen, HifB is a
periplasmic chaperone, HifC acts as an outer membrane assembly
platform, and HifD is believed to be minor pilus component (33). Recent evidence suggests that the fifth gene in the
cluster, hifE, encodes a pilus tip-associated adhesin
responsible for binding to gangliosides on the surface of mammalian
cells (3, 9). Mutations in hifE do not affect the
stability of the other pilins but severely reduce assembly of the whole
pilus (16, 17, 24, 38). For Hib strain Eagan, McCrea et al.
(17) have shown that anti-HifE antiserum binds to pilus tips
and blocks pilus-mediated hemagglutination. Conversely, van Ham et al.
(36) reported that the major pilus subunit HifA and not the
minor pilins HifD or HifE effect binding to erythrocytes and human
oropharyngeal epithelial cells. These conflicting results might be due
to the slight (20%) difference in primary sequences between the HifA
proteins studied or because of differential expression of the
recombinant H. influenzae genes in the Escherichia
coli DH5
background used in the second study. Pilus expression
by H. influenzae oscillates between phase off and phase on
at a rate of about 10
4/generation (4). This
phase variation is likely due to slip-strand mispairing in a poly(TA)
dinucleotide tract separating the divergent, bidirectional
hifA and hifBCDE promoters altering the spacing upstream of the transcriptional start sites (39).
In 1984, a unique and lethal condition caused by H. influenzae emerged in central Brazil. The disease called Brazilian
purpuric fever (BPF), afflicted young children who had recovered
earlier from conjunctivitis, causing an array of symptoms including
acute fever, petichiae, and vascular collapse (1). The
etiologic agent of BPF was found to be a clonal strain of H. influenzae biogroup aegyptius, nonencapsulated organisms in
biotype III that had previously only been known to cause self-limited
conjunctivitis. The BPF-associated reference strain, F3031, had several
characteristics not encountered in other NTHI strains, such as
endothelial cell toxicity, resistance to human serum, and the ability
to cause bacteremia in infant rats (15, 20, 22).
One possible factor in the unusual pathogenicity of F3031 is the
immunologically distinctive hemagglutinating pilus elaborated by the
strain (41). The pilus appears to be necessary for invasion of primary epithelial cells by F3031 (5). Further, BPF clone strains isolated from systemic sources are piliated more often than is
Hib (15). In a recent study we cloned and characterized genetically the F3031 pilus determinants (24). F3031 has two independently phase-variable fimbrial clusters, one of which, hif1, is in a chromosomal location not previously described
for H. influenzae (Fig. 1).
Therefore, pilus production occurs when one or both sets of genes are
in the on phase, perhaps explaining the abundant piliation of the
strain. We originally designated the F3031 genes hafA to
hafE (24), but because they are functionally similar to the H. influenzae hif cluster, we will henceforth
refer to them as hifF3031 alleles. While the
BPF-associated HifA to HifD gene products share 72 to 96% identity
with Hib proteins, the HifEF3031 putative pilus tip adhesin
has only 40% identity with its Hib homolog.

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FIG. 1.
Schematic diagram of hif1 and hif2
clusters of BPF-associated strain F3031 (24). The five pilus
genes of each cluster are indicated by open arrows, while the flanking
H. influenzae genes are indicated by gray arrows.
hif1 and hif2 are flanked by direct repeats
homologous to Rd genome coordinates (6) 1220363 to 1220394 and 1682304 to 1682362, respectively.
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The purpose of this study at its outset was to determine whether the
possession of duplicated pilus clusters and the distinctive HifE
adhesin were unique features of BPF-associated H. influenzae strains. To further this aim we examined a collection of H. influenzae biogroup aegyptius, NTHI, and capsulated H. influenzae by Southern DNA hybridization, PCR, and sequencing of
variant hifE genes.
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MATERIALS AND METHODS |
Bacteria.
The H. influenzae strains used in this
study are described in Table 1. All were
grown for 16 to 20 h on chocolate agar plates (Becton Dickinson,
Cockeysville, Md.) at 37°C in a 5% CO2 atmosphere.
PCR.
Amplifications were run for 35 cycles at an annealing
temperature of 55°C with Promega (Madison, Wis.) reagents.
Oligonucleotide DNA primers (Table 2)
were synthesized by the Emory University Microchemical Facility. We
used 15 µM Mg2+ and 30 pmol of each primer. To prepare
templates, single colonies of bacterial culture grown overnight on
chocolate agar plates were resuspended in 50 µl of sterile water and
boiled for 5 min. In a standard PCR mixture of 50 µl, 2 µl of
template was used.
Southern hybridization.
H. influenzae DNA was prepared
from cultures grown overnight on chocolate agar plates by using the
DNA/RNA Isolation Kit (United States Biochemicals). Digested DNA was
transferred to nylon membranes (31) and hybridized to
digoxigenin-labeled DNA probes with the Genius Nonradioactive Detection
(Boehringer Mannheim, Indianapolis, Ind.) reagents and protocols. The
hybridizations with labeled probe were carried out overnight at 65°C.
The final washes of the membrane were at 65°C in 0.5× SSC buffer
(1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (31).
Restriction fragment length polymorphism (RFLP)-PCR.
PCR
fragments containing hifE1 and hifE2 (products of
reactions with HE1-HI1153 or HE1-PUR pairs [Table 2]) were cut from 0.7% agarose gels, melted at 70°C in 2 volumes of sterile
H2O, and used as templates for a nested PCR with primers
HE1 and HE2. The resulting PCR products were all 1.3 kb in length from
a conserved region at the 3' end of hifD to a conserved
region at the 3' end of hifE. These DNA fragments were
digested separately with ClaI, Sau3AI,
RsaI, and DraI restriction enzymes (New England
Biolabs, Beverly, Mass.), each of which cut zero to six times.
Sequencing.
PCR amplicons containing hifE2 genes
of strains ATCC9007, GA2078, and F2066 were generated with the HE1 and
PEP primers (Table 2). The hifE1 gene of H. influenzae biogroup aegyptius F4931 was amplified with HE1 and
HI1153. The four genes were sequenced with a set of specifically
generated primers by dideoxy dye terminator cycle sequencing with an
ABI Prism fluorescence sequencing kit on an ABI Prism 377 sequencer
(Perkin Elmer). DNA sequence alignments were computed with ABI Prism
software.
Hemagglutination.
H. influenzae strains were tested
for their ability to agglutinate human O-positive erythrocytes by a
microplate assay described previously (24).
Nucleotide sequence accession numbers.
The
hifE29007, hifE2GA2078,
hifE1F4931, and
hifE2F2066 nucleotide sequences were deposited
in GenBank under accession numbers AF026299 to AF026302, respectively.
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RESULTS |
Hybridization of the hifC probe with an H. influenzae strain set.
A panel of 27 H. influenzae strains (Table 1) was probed with a conserved
hifC gene fragment in order to determine the presence of
pilus gene complexes. The probe was a 296-bp digoxigenin-labeled PCR
fragment containing a portion of the hifCF3031
locus, generated with primers HC1 and HC2 (Table 2). The
hifC gene was chosen because the encoded protein is
essential for pilus production (40) and the nucleotide
sequence is highly conserved between H. influenzae pilus
clusters (9); for example, Hib strain Eagan hifC
has 96% similarity to hifCF3031. The H. influenzae set included BPF type strain F3031; H. influenzae biogroup aegyptius F6422, a strain associated with a
BPF-like outbreak in Australia; two H. influenzae biogroup
aegyptius "Pradopolis" strains, which are indistinguishable from
F3031 by enzyme isotyping but do not express pilus; and several
non-BPF-associated H. influenzae biogroup aegyptius strains
from Brazil and Texas. Also included were representative isolates of
the six H. influenzae capsule serotypes and four nontypeable strains from the Georgia Emerging Infections Surveillance Program (formerly the Metropolitan Atlanta Active Surveillance Program). H. influenzae Rd was included as a control. The genome of Rd
has been sequenced completely and does not contain pilus genes
(6).
Southern hybridizations of the hifCF3031 probe
with H. influenzae BglII chromosomal digests are depicted in
Fig. 2. Because the probe was relatively
small (296 bp) and did not contain a BglII recognition site
and because sites for this enzyme are relatively uncommon in the
Haemophilus genome, it was likely that two bands in the
Southern hybridization represented distinct hifC alleles rather than two restriction fragments of the same gene hybridizing with
the probe. Fifty-six percent (15/27) of the strains contained at least
one hybridizing restriction fragment. Seven of the 10 H. influenzae biogroup aegyptius strains had two hybridizing
fragments. Only 1 of 10 H. influenzae biogroup aegyptius
strains, ATCC 43806, isolated in Texas, did not hybridize to the probe.
In contrast, only 2 of 5 NTHI strains and 4 of 12 typeable strains
(from a, b, and c capsule serotype strains) contained hifC
homologs. It is notable that many strains carry hif genes
but do not agglutinate erythrocytes (Table 1, footnote a),
suggesting that, like F3031 and Hib strain 770325 (24, 39),
pilus expression by these bacteria is phase variable.

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FIG. 2.
Southern hybridization of the set of H. influenzae strains with hifC-specific probe (see
Materials and Methods for details). Chromosomal DNA was digested with
BglII. The positions of DNA molecular size markers (in
kilobases) are shown on the left. Strains with two fragments
hybridizing to the hifC probe were F3031, F6422 (double
band), F4931, F4933, F2066, F3118, and ATCC 43794 (all H. influenzae biogroup aegyptius strains). H. influenzae
strains with one hybridizing BglII fragment are biogroup
aegyptius strains F3331 and ATCC 43800, NTHI strains F8835 and GA2188,
serotype a strains GA2078 and GA4774, serotype b strain 1007, and
serotype c strain ATCC 9007. The biogroup aegyptius strain F6422 and
serotype f strains GA084, GA4090 and GA4913 had extra hybridizing DNA
fragments, but because they appeared after extended exposure of the
film, they were not deemed significant.
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PCR analysis of Haemophilus gene clusters.
Next,
we determined the chromosome location of the hif genes in
the 27 H. influenzae strains on the basis of the known
positions of the hif1 and hif2 clusters of F3031
(Fig. 1). The F3031 clusters are inserted in intergenic regions between
pairs of genes, purE and pepN (hif2)
and pmbA and HI1153 (hif1), respectively, that are contiguous in the Rd genome (24). We subjected the
H. influenzae strain set to PCR with primers complementary
to the ends of the F3031 hif1 and hif2 gene
clusters (Table 2). These PCRs produced amplicons from conserved
portions of hifA and hifE (with primers HA1 and
HE1) to conserved regions flanking the hif1 (with primers PMB and HI1153) and hif2 (with primers PUR and PEP)
clusters. Table 3 shows the results of
the PCR analysis. In seven of the 27 strains, all of them H. influenzae biogroup aegyptius, PCR were successful with both
hifA1- and hifE1-specific primers, indicating the
presence of a complete five gene hif1 cluster located
between the pmbA and HI1153 open reading frames (ORFs). In
addition, H. influenzae biogroup aegyptius strain F3118
produces hifE1 and hifE2 amplicons, but neither
the hifA1 nor the hifA2 amplification product is
produced. One possible reason for this is that the HA1 primer does not
bind to sites in the hifAF3118 genes. Fifteen of
27 strains amplified with the HA1-PUR (hifA2-specific) and HE1-PEP (hifE2-specific) primer pairs, indicating the
presence of an entire hif2 cluster. With a few exceptions
(see Discussion), the number of intact pilus gene clusters deduced from
the PCRs matched the number of bands hybridizing to the hifC
gene probes (Fig. 2). Strains believed to carry two hif gene
clusters from the Southern hybridization described previously were
amplified successfully with both hif1 and hif2
primer sets, whereas strains with only one BglII fragment
hybridizing to hifC produced amplification products with
either the hif1 or hif2 primer sets. Thus there is no evidence that any H. influenzae strain contains pilus
genes situated in any location other than hif1 or
hif2.
Significant variation was noted in fragment lengths produced by
amplification with primer sets specific for the hifA2 and hifE2 genes (Table 3). The size of the HA1-PUR amplicon
varied from 0.70 to 1.35 kb; the HE1-PEP amplicon varied from 1.30 to 1.80 kb (not counting the type f strains; see Discussion). As described
below, nested PCR showed that the size of hifE was always 1.3 kb (Fig. 3), suggesting that DNA
fragment size variation is in the hifE-to-pepN
intergenic region. Except for those of F6422, the hifA1 and
hifE1 amplicon sizes were uniformly 0.95 and 1.50 kb, in
significant contrast to the variation found in the hif2 cluster.

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FIG. 3.
RFLP of hifE genes. (A) Fourteen PCR
amplicons generated with oligonucleotide primers HE1 and HI1153
(hifE1) or HE1 and PEP (hifE2). (B) These DNA
fragments were excised from the gel and used as templates for nested
PCR with HE1 and HE2. The uniformly sized hifE amplicons
were digested with four restriction enzymes. (C) ClaI
digestion of the amplicons. The sizes of DNA markers (in kilobases) are
shown on the left.
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Variation in hifE genes examined by RFLP-PCR.
We
developed a simple RFLP-PCR procedure to sample the genetic variation
of hifE in our Haemophilus strain collection
(Fig. 3). Based on digestion of nested hifE PCR products
with four restriction enzymes, there was a distinct group of alleles
from H. influenzae biogroup aegyptius strains that were
indistinguishable from, or very similar to, the duplicated
hifEF3031 genes. The H. influenzae biogroup aegyptius genes with identical restriction patterns were hifE1F2066, hifE2F4931
and hifE2F4933, while strain 43794 hifE genes differed by only one restriction site. Of the
aegyptius strains with duplicated pilus gene clusters (Table 3), F3031, F3118, and 43794 contained identical hifE1 and
hifE2 alleles. However, non-BPF-associated strain F2066 and
"Pradopolis" strains F4931 and F4933 had one hifE copy
indistinguishable from hifEF3031 but the other
was genetically quite distinct. For F2066, variation from
hifEF3031 was noted in the hifE2 gene
whereas in the "Pradopolis" strains variation occurred in
hifE1. Aside from the conserved hifEF3031 allele, no other hifE genes
shared identical or nearly identical RFLPs.
Sequence comparisons of hifE genes.
Two H. influenzae biogroup aegyptius strains with divergent
hifE genes (hifEF4931 and
hifEF2066) were selected for sequence analysis.
Both had apparently identical copies of the
hifEF3031 allele within a second gene cluster.
In addition, PCR products containing hifE2GA2078
(serotype a) and hifE29007 (serotype c) were
sequenced, as pilus genes from these H. influenzae capsule serotypes had not been described previously. The nucleotide and predicted HifE amino acid sequences of the four genes were aligned with
sequences of three hifE genes already in GenBank from strain F3031 (accession number U54780 [24]), Hib strain
770235 (accession number U19761 [38]), and NTHI strain
86-025 (accession number U19730) (Table
4). The amino acid distance matrix was
used to create a dendrogram of HifE relatedness by the neighbor joining method (30) (data not shown). The phylogenetic analysis
grouped the HifE proteins into three classes consisting of sequences
from F3031 (BPF), 9007 (serotype c), and F4931 (H. influenzae biogroup aegyptius "Pradopolis") in the first
group; GA2078 (serotype a), F2066 (non-BPF H. influenzae
biogroup aegyptius), and 86-025 (NTHI) in the second group; and Hib
strain 770235 in a group of its own. The HifE sequence of Hib did not
have more than 54% similarity with any other encoding nucleotide
sequence or 45% similarity with any other protein sequence (Table 4).
Significantly, hifE1F4931 and
hifE2F2066 were only 77% and 44% similar,
respectively, to hifEF3031 despite having an
apparently identical hifE gene on a second pilus gene
cluster. The F2066 HifE protein had much more sequence similarity with
HifE from NTHI and H. influenzae type a than with the two
other H. influenzae biogroup aegyptius protein sequences
(Table 4).
Alignment of the HifE sequences (Fig. 4)
demonstrated similarities in the C-terminal region, including 14 identical amino acids at the end of each molecule. The C terminus of
HifE is homologous to those of HifA and HifD and of other pilins from
Pap and type I pili (9, 16). This region is required for
binding of the pilus-specific periplasmic chaperone, which is necessary
for correct assembly of the pilus fibers (33, 42). In
contrast to the C terminus, the N-terminal two-thirds of the proteins
had little conserved sequence. Particularly striking were the predicted
signal peptides (Fig. 4), which are distinctive to each of the three groups of HifE arranged by overall sequence similarity. Despite extensive sequence diversity, the N-terminal portion included a series
of short, highly conserved amino acid motifs (Fig. 4). A search of the
SWISSPROT database revealed that these conserved motifs in the N
terminus of HifE aligned with nearly identical spacing to conserved
domains in the N terminus of PilC, the putative Neisseria
pilus-associated adhesin (23) (Fig.
5). This result raises the possibility
that the conserved motifs might be necessary for recognition of a
mammalian cell receptor common to Neisseria and
Haemophilus. The HifE motifs did not match the motifs of any other proteins in the database, including HifA and HifD sequences. No
other regions of the PilC proteins, with an average size of about 1,040 amino acids, showed significant homology to HifE.

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FIG. 4.
Alignment of H. influenzae HifE amino acid
sequences. The amino acid sequences of Hib strain 770235 and
BPF-associated strain F3031 were published by van Ham et al.
(39) and Read et al. (24), respectively. The
sequence of NTHI strain 86-025 was obtained from GenBank (accession no.
U19730). Other sequences were reported in this study. Residues
conserved between the seven proteins are shown in the last line each
block (consensus). Dashes indicated gaps introduced by the alignment
program. The highly conserved C-terminal region of the HifE proteins
following the last cytosine residue is shaded. Predicted signal
peptidase cleavage sites are illustrated with an arrow ( ). The three
groups of variant signal peptides are boxed separately. Three conserved
domains in the N terminus of the proteins with similarities to the
Neisseria PilC sequence are underlined. Residues in these
domains similar to the PilC consensus are shown in bold type.
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FIG. 5.
Comparison of HifE domains with Neisseria
PilC proteins. The alignment of PilC proteins is taken from the study
by Rahman et al. (23). A portion of the N terminus of each
of six PilC proteins from residues 124 to 270 is aligned against the
three HifE conserved regions underlined in Fig. 4. PilC residues in
bold are conserved within all six proteins and share similarity to the
HifE domain. In two cases phenylalanine residues (f) are typed in lower
case where they match tyrosine residues in PilC. N. meningitidis (NM) FAM120 PilC1, FAM120 PilC2, and A1493 PilC
(24, 29) have been assigned EMBL accession numbers Y13020,
Y13021, and Z54202, respectively. N. gonorrhoeae (NG) MS11
PilC1, MS11 PilC2 and GC-640 PilC (13, 24, 28) have been
assigned EMBL accession numbers Z50180, Z49120, and Z54202,
respectively.
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DISCUSSION |
Several findings about H. influenzae pili emerge from
the data presented in this paper. First, the presence of two complete hif gene complexes and the hifEF3031
allele are common in H. influenzae biogroup aegyptius and
not just limited to BPF-associated strains. Second, many H. influenzae strains contain partial sets of hif genes,
or do not appear to have any genes, at the hif1 and
hif2 chromosome location. In this study, a broad range of
H. influenzae strains, including biogroup aegyptius, NTHI,
and capsule serotypes a, b and c, were found to carry complete
hif pilus clusters. Similar host ranges were reported in
previous surveys with Hib or NTHI hifA probes (2, 7, 8,
14). A third finding is that HifE protein sequences can be
classed into at least three subfamilies, with members sharing at most
50% identity with proteins from other groups and with each subfamily
having a specific N-terminal signal sequence. Finally, we identified
conserved motifs in the N-terminal portion of HifE that match conserved
domains in the N terminus of the neisserial pilin PilC.
Previous work (24, 35) showed that Brazilian BPF isolates
contained two sets of pilus genes. As abundant piliation is a feature
of BPF-associated H. influenzae isolated during the systemic
phase of infection (1), we speculated that the duplicated pilus configuration was an important adaptation to pathogenesis. This
survey indicates that several non-BPF-associated H. influenzae biogroup aegyptius strains, as well as BPF-associated
strain F3031, carry two complete pilus complexes. Besides aegyptius
strains, no other group of H. influenzae tested contained
two entire sets of hif genes. It seems, therefore, that two
pilus complexes are a common feature of H. influenzae
biogroup aegyptius but not specific to BPF-causing biogroup aegyptius.
The pilus cluster duplication event might have occurred in an ancestor
common to many H. influenzae biogroup aegyptius isolates.
Identifying evolutionary relationships between H. influenzae
bacteria containing hif1 might provide information on the
genetic determinants responsible for the enhanced pathogenesis of the
BPF-associated strain. The two pilus complexes might also be an
adaptation to conjunctival colonization or infection. If piliation is
important for BPF infection, then the regulation of expression of the
hif genes in addition to pilus gene copy number is
important. It is notable that "Pradopolis" strains F4931 and F4933,
related to F3031 by enzyme isotyping and shown by this study to contain
two complete clusters, did not elaborate hemagglutinating pilus under
laboratory conditions (22).
Some H. influenzae strains in this study appear to contain
hifA or hifE homologs in truncated copies of the
fimbrial cluster as well as complete pilus complexes. Strains F8835
(NTHI), GA2078 (serotype a) and ATCC 9007 (serotype c) are templates
for the hifA1-specific primer pair but not for the
hifE1 primers. These strains contain only one
hifC homolog (Fig. 2) nd appear to have a complete hif2 complex due to amplification with
hifA2 and hifE2 primers, hence the possibility
they contain partial clusters with at least the hifA1 gene
but not hifC1. Australian H. influenzae biogroup
aegyptius strain F6422 appears to have two hifC genes by
Southern analysis (Fig. 2), but the hifA1-specific primers produce a smaller amplicon than do other strains and
hifE1-specific PCR gives a negative result. Perhaps the
hifE1-specific primers have too little homology to bind, or
alternatively, F6422 contains an incomplete cluster in the
hif1 location that includes portions of the hifA
and hifC genes. Likewise, H. influenzae biogroup
aegyptius strain ATCC 43806 might have an incomplete copy of the
hif2 genes as hifA2 but not hifE2 PCR
products are amplified. Lastly, serotype f strains GA840, GA4090, and
GA4913 do not hybridize to the hifCF3031 probe
but produce amplicons with hifA2- and
hifE2-specific primers (Table 3). The small size of the
hifE2 PCR product (0.45 kb) suggests a deletion in this
gene. These incomplete H. influenzae pilin gene clusters may
be nonfunctional remnants, or they might have one of two intriguing
possible roles. The genes might express pilin subunits that can be
assembled into the fimbriae encoded by the other cluster to promote
variation in the surface-exposed protein. Alternatively, the pilin
genes in the abbreviated pilus cluster might effect antigenic variation
by recombining with the expressed loci of the second complex in a
manner analogous to the silent pilin genes of Neisseria
(26).
We used a simple RFLP-PCR method in order to establish relationships in
the 21 hifE alleles identified by PCR. Because only a
relatively small number of restriction sites were used for typing, the
technique was more useful for detecting genes with very similar nucleotide sequences than for enabling accurate estimations of genetic
distance. One striking result was the conservation of the
hifEF3031 allele among BPF- and
non-BPF-associated H. influenzae biogroup aegyptius strains,
indicating again that the F3031 pilus is not a characteristic unique to
strains causing BPF. However, apart from the group similar to
hifEF3031, no other pairs of hifE genes showed significant similarity by this crude test. This
variability was reflected in the nucleotide sequences of four
hifE genes determined in this work and three already in the
GenBank database. No gene had more than 80% similarity to another, and
the majority shared only 40 to 55% identity (Table 4). Classification
of the predicted amino acid sequences by relatedness revealed that the
HifE from Hib is the sole member of one of three groups that shared
less than 50% overall similarity. The other groups both included HifE from serotypes a and c and NTHI. It is interesting that H. influenzae biogroup aegyptius proteins are grouped with those of
H. influenzae type c, as isolates of this capsule serotype
have been aligned phylogenetically with the Brazilian BPF clone
(18).
H. influenzae biogroup aegyptius strains F2066 and F4931
appear to have one copy of hifEF3031 and a
second highly divergent hifE allele, with similarities to
genes from H. influenzae capsule serotypes a and c. In
contrast, biogroup aegyptius strains F3031, F3118, and 43794 have
copies of hifE that are indistinguishable by RFLP-PCR. Amino
acid sequence divergence in HifE2F2066 and HifE1F4931 does not appear to have originated from
localized recombination events between hifE genes as was the
case, for example, for the H. influenzae genes encoding type
1 immunoglobulin A1 proteases (21). Inspection of aligned
hifEF3031, hifE1F4931,
and hifE2F2066 revealed nucleotide
substitutions, deletions, and insertions distributed more or less
randomly through the divergent 5' two-thirds of the sequences rather
than concentrated in any specific portion of the genes (data not
shown).
By comparing the divergent HifE sequences (Fig. 4), we identified
conserved domains that might contribute to the function of the protein.
In PapG and other related fimbrial adhesins, the N-terminal portion is
necessary for binding to mammalian cell receptors (11, 32).
The N terminus of HifE consists of a series of short, highly conserved
domains interrupted by regions with little similarity (Fig. 4). That
the HifE domains play some part in the recognition of mammalian cell
receptors is suggested by their conspicuous similarity with portions of
the Neisseria PilC protein (Fig. 5). PilC is a minor
component of the type IV pilus that confers epithelial cell binding
proficiency (19). Neisseria species commonly
carry two genes, pilC1 and pilC2. Both copies function in pilus biogenesis, but only pilC1 is necessary
for adhesion of N. meningitidis to certain human endothelial
and epithelial cell lines (19). The exact role of PilC is
still in question; the protein might act as a tip-associated adhesin
(27) or, alternatively, might be located in the outer
membrane and involved in processing of the pilus to an adhesive form
(23).
This study provides interesting insights into the role of pilus in the
biology of H. influenzae. Pili allow the bacterium to attach
to certain epithelial cells (10, 29, 34), but it is unclear
whether they are necessary for nasopharyngeal colonization (9). As colonization is vital for persistence of H. influenzae, the pilus might be a highly specialized structure,
useful for exploiting a limited number of specific environments.
Current information on H. influenzae pilus genetics adds
weight to this idea. Fimbrial expression is phase variable, which
implies that, in certain microenvironments at least, nonpiliated
organisms survive in their human host. Also, the results of this study
suggest that a significant portion of H. influenzae strains
contain no hif-related pilus genes at all. Possibly there is
flux in the H. influenzae population, with strains deleting
pilus genes when there is no selective pressure and reacquiring them
through natural transformation. Insertion of pilus clusters has been
inferred from sequencing data: hif1 and hif2
genes are flanked by pairs of genes that are contiguous in the
pilus-negative Rd strain and the junctions contain extended direct
repeats and multiple copies of an H. influenzae repetitive
extragenic palindrome-like element (24, 25, 38). This work
also documents extensive variation of the hifE putative adhesin gene sequences. There are two likely reasons for this variability. First, genetic changes might generate variable epitopes on
the surface-exposed protein, allowing H. influenzae to avoid the host immune response mounted against the pilus. The second explanation for variation of HifE is to allow attachment of the pilus
to novel mammalian cell receptors. A structure-function relationship
for HifE-mediated adhesion during infection could explain why certain
hifE alleles are highly conserved among isolates from
different locations and times, such as hifEF3031
and hifEHib. Identification of conserved and
variable domains in the N terminus of HifE and similarities to another
putative adhesin in Neisseria is an important first step in
dissecting the relationship between the primary sequence of the protein
and function as an adhesin in disease-causing isolates of H. influenzae.
 |
ACKNOWLEDGMENTS |
We thank Fred Quinn for providing strains, William Shafer for
critical reviews of the manuscript, and Tara Dove, Cynthia Gordon, and
Samantha Terris for technical support and help with preparing the
manuscript.
This work was funded by a Veterans Affairs Merit Award to M.M.F.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Atlanta VA
Medical Center, Medical Research Service 151, 1670 Clairmont Rd.,
Decatur, GA 30033. Phone: (404) 728-7688. Fax: (404) 329-2210. E-mail: mfarley{at}emory.edu.
Editor: J. G. Cannon
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Infect Immun, April 1998, p. 1622-1631, Vol. 66, No. 4
0019-9567/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
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