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Journal of Bacteriology, December 2003, p . 7285-7290, Vol . 185, No . 24
Differences in Genetic and Transcriptional Organization of the glpTQ Operons between Haemophilus influenzae Type b and Nontypeable Strains
Xin-Ming Song1 and Håkan Janson2*
Vaccine
& Infectious Disease Organization, University of Saskatchewan,
Saskatoon, Saskatchewan, S7N 5E3
Canada,1
Department of Medical
Microbiology, Lund University, Malmö University Hospital, S-205
02 Malmö, Sweden2
Received 6 June 2003/
Accepted 25 September 2003
The
glpTQ operon of Haemophilus influenzae type b (Hib)
and nontypeable H . influenzae (NTHi) strains is highly
conserved, except for a 1.4-kb glpTQ intergenic region that
was found in most Hib strains . The presence of this intergenic region
results in divergent glpTQ transcriptional profiles for Hib
and NTHi where Hib strains appear to have evolved an alternative
promoter for glpQ expression . Based on the intergenic
region's low G+C content, we speculate that this DNA
fragment was acquired by lateral
transfer .
Haemophilus influenzae is a common pathogen, especially among
children, but the clinical manifestations are largely type specific.
The encapsulated H . influenzae serotype b (Hib) usually causes
invasive infections, such as meningitis and septicemia
(2), whereas the much more
common nonencapsulated, or nontypeable, H . influenzae (NTHi)
is a major cause of otitis media, sinusitis, and pneumonia
(8) . General vaccination
against Hib has reduced the incidence of Hib infection to a near
minimum (10), while
attempts to construct a vaccine against the costly NTHi infections have
as yet been unsuccessful due to a high genetic heterogeneity among NTHi
strains (20) . An
extensively studied virulence factor and potential vaccine candidate in
H . influenzae is protein D, a 42-kDa conserved lipoprotein
expressed on the bacterial surface
(1,
13,
21,
24) . An isogenic protein
D-negative mutant has been shown to be less effective than its
wild-type parental strain in its ability to (i) cause experimental
otitis media in rats
(14), (ii) cause damage
to ciliated human respiratory epithelium
(15), and (iii) promote
internalization into human monocytic cells
(17) . The mechanism
behind the virulence properties of protein D is unknown but may involve
choline decoration of H . influenzae lipooligosaccharides
(LOS), since protein D expression allows H . influenzae to
obtain choline from cocultured host cells and subsequently incorporate
this molecule into its LOS
(6) .
The
ability of protein D to promote the incorporation of choline into LOS
comes from its glycerophosphodiester phosphodiesterase activity,
catalyzing the hydrolysis of glycerophosphodiesters into
glycerol-3-phosphate (G3P) and an alcohol
(14,
18) . The gene encoding
protein D (hpd) is homologous to glpQ of
Escherichia coli
(16) and other bacteria.
The glpQ gene belongs to the glp regulon that is
involved in the utilization of glycerol and of G3P and its precursors
as energy sources and to supply precursors for phospholipid
biosynthesis . In E . coli and Bacillus
subtilis (19),
glpQ is transcribed together with glpT, which is
located upstream of glpQ and encodes a G3P permease that acts
as a G3P-inorganic phosphate antiporter
(5) . The E . coli
glpTQ operon is induced by G3P and repressed by the catabolic
repressor glucose as well as a glp-specific repressor protein,
GlpR (28) . Available
restriction fragment length polymorphism (RFLP) data and DNA sequences
of the glpTQ region of H . influenzae suggest that its
organization differs between strains
(7,
13,
24,
25) . RFLP analysis based
on a combination of two restriction endonucleases and two probes
complementary to the glpQ gene of H . influenzae
(hpd) showed that the majority of Hib strains (34 of 39) carry
the glpQ gene on a 3.3-kb fragment between two conserved
PstI sites (Fig.
1), whereas 24 of 35 NTHi strains display only a 1.9-kb fragment between
the same PstI sites
(13) . As in the case of
E . coli and B . subtilis, glpT in most NTHi
strains is located immediately upstream of glpQ
(12,
13,
24) . By contrast,
glpT and glpQ are separated by a 1.4-kb fragment of
unknown function in the majority of Hib strains and some other
encapsulated H . influenzae strains, including strain Rd (Fig.
1)
(7,
13,
24,
25) . The present study
was designed to characterize and compare the genetic structures and RNA
transcriptional profiles of the glpTQ region in H.
influenzae strains and to elucidate the potential function of the
1.4-kb glpTQ intergenic region that is present only in
encapsulated H . influenzae strains .
| FIG . 1 . Schematic
genetic map of the glpABC, glpTQ, and glpFK
operons in H . influenzae Rd
(7) and genetic map and
RNA transcript analysis results of the glpTQ operons of Hib
HK695, Hib Eagan, Eagan-derived 1.4-kb glpTQ intergenic region
mutant Ekm1, and NTHi 772 . Arrows labeled with gene names and ORFs
denote transcriptional orientations . Potential transcriptional
termination loop structures are marked with circles . Conserved
restriction endonuclease sites are indicated . RNA transcripts detected
by Northern blotting or RT-PCR are marked under the respective genes or
ORFs with thick and fine lines,
respectively.
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DNA
sequence analysis.
In
addition to using previously reported sequences
(12,
24,
25), we used sequences
determined in the course of this study, namely, the entire DNA
sequences of the glpTQ operons of Hib Eagan and NTHi 772, as
well as the 1.4-kb glpTQ intergenic region of Hib HK695
(26) . The
1.4-kb glpTQ intergenic regions of Hib Eagan and HK695 were
cloned into pBluescript II KS by excising a 2.2-kb
PstI-EcoRI fragment (Fig.
1) from plasmids pXME10
and pXMHK10, which harbor the 3.3-kb PstI
fragments that were used to clone the hpd genes
(24) and subsequently
transformed into E . coli XL1-Blue . Nested deletions with
exonuclease III and mung bean nuclease
(22) were performed after
a SacI-XbaI digestion of the resulting plasmids,
pE1.4pe1 and pHK1.4pel, and on KpnI-BamHI-cleaved
pXME10 and pXMHK10, respectively . The DNA sequences of the 1.4-kb
intergenic regions of Eagan and HK695 were determined in both
orientations from the constructed nested deletion plasmids with vector
primers M13-u and M13-r (Table
1) by using an Applied Biosystems 377 automatic sequencer . The DNA
sequences of glpT and the glpTQ intergenic region of
NTHi 772 were determined from a 2.0-kb PCR product amplified with
primers glpA-1 and hpd-10 (Table
1) and sequenced with
primers specific for the glpT gene of Hib Eagan
(25) . The DNA
sequence upstream of glpT of Hib Eagan was obtained from a PCR
amplicon by using primers glpA-1 and glpT-9 (Table
1) .
| TABLE 1 . Oligonucleotides
used in this study
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The
glpT sequences of Hib Eagan and NTHi 772 were almost as highly
conserved as the previously sequenced glpQ gene
(13,
24) . The glpT
genes from the two strains differed in 15 bp and displayed identical
deduced amino acid sequences of the same length . The regulatory region
upstream of the NTHi 772 glpT gene was also identical to the
corresponding region of Eagan, except that 772 contained one extra base
pair located 91 bp upstream of the glpT start codon (Fig.
2) . Potential catabolic and transcriptional regulation sites with
homology to consensus sequences upstream of glpT in E.
coli were also found upstream of glpT in Eagan and 772.
They include two catabolic activator protein binding sites
(4), two operator sites
with the potential of binding to the E . coli glp repressor
protein (29), and a
sequence homologous to the integration host factor (IHF)
(9) (Fig.
2) . The binding of IHF to
this site may bend the DNA to facilitate the formation of a complex
structure that is involved in the inhibition of GlpT expression,
mediated by the GlpR repressor in E . coli
(28) . However, despite
the existence of two GlpR homologues, no homologues of ihfA
and ihfB (R . A . Weisberg, M . Freundlich, D.
Friedman, J . Gardner, N . Goosen, H . Nash, A . Oppenheim, and J.
Rouvière-Yaniv, Letter, Mol . Microbiol . 19:642, 1996) have
been identified in the H . influenzae Rd genome
(7) .
| FIG . 2 . Nucleotide
sequence alignment of the glpT promoter region of H.
influenzae Rd (7),
Hib Eagan, and NTHi 772 . The numbered positions of nucleotides refer to
the Rd genome . A sequence gap is indicated with the symbol ¤.
The glpT and glpA start codons are indicated in
boldface and italics, and arrows mark the transcriptional directions.
Putative -10 and -35 sequences are underlined with
double and single solid lines, respectively . Proposed catabolic
activator protein (CAP), IHF, and operator binding (O) sites
are indicated with dashed arrows above the sequences . Potential
promoter sites (P) for the glpT genes of Eagan and
772, based on the primer extension assay, are marked with vertical
arrows.
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In the
glpTQ intergenic region, both Hib strains contained
practically identical 1,428-bp sequences, except that HK695 contained
one more tetrameric repeat (TTTA) in addition to the five repeats
present in Eagan . The repeats were localized in a putative open reading
frame (ORF) of 414 bp in HK695, designated ORF1 for these Hib strains
(Fig . 1) . The lack of one
tetramer in Eagan caused a frameshift that led to a stop codon after
228 bp and resulted in two smaller ORFs (Fig.
1) . Most tetrameric DNA
repeats in H . influenzae have been associated with the
regulation of potential virulence factors such as iron acquisition
factors, adhesion molecules, and LOS biosynthesis
(11,
27), but the function of
ORF1 is unknown . Another putative 390-bp ORF (ORF2) of the Hib
glpTQ intergenic region was found immediately upstream of
glpQ (Fig . 1).
The glpTQ intergenic region of the two Hib strains was highly
homologous to the corresponding region of H . influenzae Rd
(7) . Two ORFs with unknown
functions, HI0687 and HI0688, correspond to ORF1 and ORF2 of the Hib
strains with the exception that HI0687 of H . influenzae Rd
exhibits a larger size than ORF1 (Fig.
1) . The G+C
contents of the 1.4-kb glpTQ intergenic region of the Hib
strains was approximately 26%, which is much lower than the
average of 38% for the glpT and glpQ genes and
39% for the H . influenzae Rd genome in general.
Although no typical insertion-like sequences were found in this region,
the 1.4-kb fragment might have been acquired by lateral transfer from
an organism with a lower G+C content . The glpTQ
intergenic region of NTHi 772 was only 103 bp long, out of which the
first 52 bp was homologous to the glpTQ intergenic regions of
the Hib strains Eagan and HK695 . This homologous part contains an
inverted repeat sequence with the ability to form a typical hairpin
loop structure exhibiting a lowest free energy value of -9.8
kcal/mol (23) that may
function as a potential transcription terminator for glpT
expression . A similar conserved inverted repeat sequence was also
identified immediately downstream of the glpQ stop codon in
both Hib and NTHi strains (Fig.
1) . This potential
glpQ transcriptional terminator exhibited a lowest free energy
value of -16.8 kcal/mol
(23) .
Construction
of a 1.4-kb mutant in H . influenzae.
Reverse PCR with a Pwo PCR kit
(Roche Diagnostics) was used to amplify the fragment flanking the
1.4-kb intergenic region of pXME10 with primers Hibup-3 and Hibup-4
(Table 1), resulting in a
1.2-kb deletion of the 1.4-kb intergenic region . The PCR product was
ligated to the 1.3-kb kanamycin resistance (Kmr) cassette
excised from pUC4K (Amersham Pharmacia Biotech) with HincII,
and the ligation mixture was transformed into E . coli
DH5 . Following the excision of the vector backbone by
BamHI-SphI cleavage, the 3.5-kb linear DNA fragment
was transformed into Eagan for homologous recombination
(14) . The chromosomal DNA
of five Kmr colonies was examined by Southern hybridization
with digoxigenin (Roche Diagnostics)-labeled probes . The glpT
and glpQ probes were labeled by PCR using a pXME10-derived
nested deletion and pHIC348
(12) as templates with
M13-u-glpTx1 and
hpd-6B-hpd-4 (Table
1)
(24) as primer pairs,
respectively . The kanamycin probe was labeled by random priming from
the gel-purified Kmr cassette that had been excised from
pUC4K with HincII . Southern blot analysis (data not shown) of
EcoRI- or HaeIII-digested chromosomal Hib DNA
revealed that the Kmr cassette had been inserted just
downstream of the glpT coding region (Fig.
1) in all tested
Kmr clones . The growth rate of one such mutant, Ekm1, was
compared to that of the parent strain Eagan, and metabolic fingerprints
were analyzed with GN MicroPlate and ES MicroPlate kits
(Biolog, Hayward, Calif.) either in brain heart infusion
broth supplemented with NAD and hemin or in the chemically defined
BCM1 medium
(25) . No significant
difference in cell densities, generation times, or metabolic properties
was observed for triplicate experiments (data not
shown) .
Characterization of promoter
positions of the glpTQ operons.
Primer extension analysis
(22) was applied to
identify potential transcriptional start positions by using antisense
DNA primers (Table 1) that
bound just downstream of the respective start codons . Primers were
labeled with [ -32P]ATP by T4
polynucleotide kinase (Amersham Pharmacia Biotech) and were used for
the extension of 40 µg of total RNA, prepared with an RNeasy
kit (QIAGEN) from cultures grown in supplemented brain heart infusion
broth . Labeled products were analyzed on a 6% polyacrylamide gel
containing 7 M urea in a Sequi-Gen sequencing cell (Bio-Rad
Laboratories) . The signal in the gel was measured either by exposure to
X-ray film or by a PhosphorImager and analyzed with ImageQuant software
(Molecular Dynamics) . A total of four bands, designated P1 to P4,
corresponding to potential transcriptional start positions of
glpT were detected in NTHi 772, whereas only three bands were
detected in Hib Eagan (P1, P2, and P4) (Fig.
2) . The lack of P3 in Hib
Eagan was unexpected since potential corresponding -10 and
-35 promoter sequences were found in both strains . The
existence of one more promoter (P3) in 772 suggests that the regulation
conditions and expression levels of glpT might differ for NTHi
and Hib strains . This hypothesis was supported by the observation that
glpT of NTHi 772 that was cloned into the pACYC184-based
vector pSU18 (3) failed to
complement the G3P uptake levels in the Hib Eagan glpT
rec-1 double mutant ETM22r2 (unpublished data), although both
strains contain almost identical glpT genes . We further
analyzed the total RNA of ETM22r2 that had been transformed with pXMS1
(25), carrying Eagan
glpT plus a partial regulatory region ending 156 bp upstream
of the glpT start codon cloned into pSU18 . Only one band
corresponding to position P1 was found (data not shown), although the
P2 site and its putative -10 promoter sequence plus the region
where a -35 consensus sequence normally is found (Fig.
2) was included in pXMS1.
This result suggests that the P1 site may be essential for
glpT transcription in Eagan since pXMS1 is able to complement
the glpT mutant ETM22r2 to a higher level of GlpT expression
than that of the wild-type strain, Eagan
(25) . It also indicates
that the signal at the P2 site in primer extension analysis may be a
degradation product of a glpT mRNA initiated from the upstream
promoter site P4 . Since ETM22r2 is a glpT mutant that was
created by the selection of spontaneous fosfomycin-resistant Hib Eagan
clones (25), it is likely
that the P4 promoter site probably exists in ETM22r2 . No signal from P4
could be detected in ETM22r2(pXMS1), which may be due to the fact that
this potential signal is too weak in comparison to the P1 signal from
the medium-copy-number plasmid pXMS1 . When potential promoter sites for
glpQ were analyzed, only one band was identified 28 bp
upstream of the glpQ start codon in Hib Eagan as well as in
E . coli(pXME10), which contains glpQ from Eagan . A
primer extension product was found 64 bp upstream of the glpQ
start codon in NTHi 772 and from E . coli(pHIC348), which
contains glpQ from 772 (data not shown) . The transcriptional
start of Hib Eagan ORF1 in the glpTQ intergenic region was
mapped to 59 bp upstream of the ORF1 start codon for both Eagan and
E . coli harboring pXME10 (data not shown) . Since the
glpTQ intergenic region of NTHi 772 is only 103 bp, the
potential transcriptional starts of NTHi 772 glpQ and Hib
Eagan ORF1 must be located within 1 bp from each other in relation to
the ends of their respective glpT genes . Both promoters share
the same putative -10 and -35 sequences, which are
situated within the loop structure downstream of glpT.
Furthermore, in spite of the divergent sequences immediately upstream
of the glpQ start codons of Eagan and 772
(24), the two strains
appear to share the same putative ribosomal binding site . Attempts to
locate a transcriptional start for ORF2 of the 1.4-kb region were
unsuccessful, but two bands were found within the ORF2 coding region
for both Eagan and E . coli harboring pXME10 (Fig.
3) . These were located 85 and 89 bp, respectively, downstream of the ORF2
start codon . Shared putative -10 and -35 sequences were
also found upstream of these sites .
| FIG . 3 . Primer
extension analysis of potential ORF2 transcriptional start positions
(indicated by arrows) of total RNAs of Hib Eagan and E . coli
harboring pXME10 by using primer Hibup-11 . The DNA ladder (T, G, C, and
A from left to right) was obtained from pXME10 that had been sequenced
with Hibup-11 and separated in the same polyacrylamide
gel.
| |
RNA
transcript analysis.
glpT (1.4 kb) and
glpQ (1.1 kb) transcripts from the total RNAs of NTHi 772, Hib
Eagan, and ETM22r2(pXMS1) were visualized by using Northern
hybridization (25) (Fig.
4) . Hib Eagan and ETM22r2(pXMS1) displayed a single band for
glpT and glpQ, respectively . NTHi 772 exhibited a
band of approximately 2.6 kb that hybridized to both glpT and
glpQ probes in addition to the respective smaller bands that
were detected in Eagan . The possibility that monomeric glpT-
and glpQ-specific bands are a result of the mRNA processing of
the larger 2.6-kb transcript cannot be ruled out, but since E.
coli harboring pHIC348 expresses GlpQ from its endogenous NTHi 772
promoter (12), and since
we successfully mapped the glpQ promoter with primer extension
analysis, it is concluded that the glpQ gene of NTHi 772 is
partially cotranscribed with glpT . No variation in mRNA
lengths due to alternative transcriptional start points was detected by
Northern blot analysis . Based on the assumption that the hairpin loop
structure immediately downstream of the glpT stop codon
terminates the glpT transcription in Hib Eagan, we examined
the glpTQ transcription patterns of the Eagan 1.4-kb mutant
Ekm1, in which the loop structure was destroyed during mutant
construction (Fig . 1 and
4) . Two Ekm1 transcripts
(2.7 and 3.9 kb) were found hybridizing to the glpT probe . It
is likely that the 2.7-kb band is a combination of the 1.4-kb
glpT and the 1.3-kb Kmr cassette and that the
3.9-kb fragment is the 2.7-kb band plus the downstream 1.1-kb
glpQ transcript . In addition to the 1.1-kb glpQ
transcript, the 3.9-kb fragment was also found when the same blot was
reprobed with a glpQ probe, suggesting that glpT
transcription could continue downstream once the loop structure was
removed . However, the practically identical loop structure downstream
of 772 glpT only partially terminated glpT
transcription because a cotranscribed glpTQ transcript was
found in this strain . We therefore conclude that a complete
interruption of the glpTQ cotranscript requires the existence
of the 1.4-kb glpTQ intergenic region .
| FIG . 4 . Northern
blot analysis of glpT- and glpQ-specific transcripts
of total RNAs of NTHi 772, Hib Eagan, Eagan-derived 1.4-kb
glpTQ intergenic region mutant Ekm1, and the cloned
glpT gene in ETM22r2(pXMS1) . The same membrane was probed with
the glpT probe and reprobed with the glpQ probe
(indicated at the bottom of the blots) after the membrane was stripped.
The molecular sizes (indicated between the blots) were estimated
according to the RNA ladder separated in the same
gel.
| |
As we failed to
detect any signals by using ORF1 or ORF2 probes in Northern
hybridization (data not shown), RNA transcripts of the 1.4-kb
intergenic region of Eagan were further characterized with reverse
transcription (RT)-PCR by using Ready-To-Go beads (Amersham
Pharmacia Biotech) and different combinations of RT-PCR primers (Table
1) . An RNA transcript that
covered the entire ORF1 and the ORF1-ORF2 intergenic region was
identified, whereas another was found covering most parts of ORF2 (Fig.
1), corresponding to the
potential promoter positions found 85 to 89 bp within ORF2 in our
primer extension assay . This latter ORF2 transcript appeared to be
cotranscribed with the downstream glpQ . This result is in
contrast to the 1.1-kb glpQ transcript previously identified
by Northern hybridization and to the potential promoter positions of
glpQ obtained by the primer extension assay, but as we could
detect the transcriptional signal only by RT-PCR and not by Northern
blotting, it is assumed that the transcription level of this
alternative glpQ promoter situated within ORF2 is low . ORF2
may act as a transcription regulatory region for glpQ in Hib,
since it is located immediately upstream of the glpQ coding
region, separated by only 11 bp . No apparent catabolic regulation
sequence homologues were found in this region . We could not find any
putative catabolic regulation sites upstream of NTHi 772 glpQ
either, but its putative promoter, found in the primer extension
analysis, is located at practically the same position as the potential
promoter of ORF1 in Hib Eagan . We therefore speculate that Hib strains
that contain the 1.4-kb fragment between glpT and
glpQ have evolved an alternative promoter region for
glpQ transcription and that the old glpQ promoter now
serves as a promoter for ORF1 . The transcriptional level of Hib ORF1
appears to be low, since an ORF1 mRNA was detected only by RT-PCR
analysis, whereas an NTHi 772 glpQ mRNA was detectable by
Northern blot analysis . The promoters are located 1 bpapart within the potential transcriptional terminator loop for
glpT (Fig . 1),
but it is unlikely that this difference would be the explanation for
the observed differences in transcriptional levels between these
promoters . The regulation of the Eagan glpQ gene is unknown
because it transcribed independently of glpT, whereas the
regulation of the glpQ gene in NTHi 772 might be dependent
upon the cotranscribed upstream glpT gene .
Overall, this
study shows the effect the presence of the 1.4-kb glpTQ
intergenic region that exists only in Hib and other encapsulated H.
influenzae strains has on glpT and glpQ
transcription in these strains compared with their transcription in
NTHi 772 . For NTHi strains, the glpQ gene (encoding the
virulence factor protein D) was in part cotranscribed and possibly
coregulated with the upstream glpT gene, encoding G3P
permease, and in part transcribed by a promoter that is situated within
a hairpin loop structure . In Hib strains, the same promoter appears to
transcribe at least one unique ORF (ORF1) that may have the ability to
phase vary its expression due to the variation of the number of
tetramer repeats situated within the ORF . It would be very interesting
to further study and determine how the regulation of genes in the
glpTQ region of NTHi strains differs from that in Hib strains
and to investigate what role the ORFs in the 1.4-kb intergenic region
of Hib strains have in
pathogenesis .
Nucleotide sequence
accession numbers.
The entire
DNA sequences of the glpT gene of NTHi 772, as well as the
1.4-kb glpTQ intergenic region of Hib Eagan and HK695
(26), were determined in
this study and submitted to GenBank under the following accession
numbers: for the 1.4-kb intergenic region of Eagan, accession no . AF132899;
for the 1.4-kb intergenic region of HK695, accession no . AF132900;
and for glpT of NTHi 772, accession no.
AF132901 .
We thank
Arne Forsgren for generous support and critical review, Christel Ekman
for DNA sequencing, and Elisabeth Glatz of the Department of
Microbiology and Andreas Hillarp of the Department of Clinical
Chemistry, Lund University, for technical assistance in the RNA
analyses .
This work was supported by grants from the Alfred
Österlund Foundation, the Malmö Medical Services
Foundation, and the Forssmans
Foundation .
* Corresponding
author . Mailing address: Department of Medical Microbiology, Lund
University, Malmö University Hospital, S-205 02 Malmö,
Sweden . Phone: 46 (40) 331321 . Fax: 46 (40) 336234 . E-mail:
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