Professional Documents
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Correspondence
thomas.boren@umu.se
In Brief
Helicobacter pylori binds with high
affinity to ABO/Leb blood group antigens
to persist in the stomach mucosa.
Bugaytsova et al. show that adherence is
acid sensitive, fully reversed when acidity
is decreased, and controlled by BabA
adhesin proteins pH-sensors sequences
changes in which are selected during
chronic infection and disease.
Article
1Department of Medical Biochemistry and Biophysics, Umea University, 901 87 Umea, Sweden
2Department of Applied Physics and Electronics, Umea University, 901 87 Umea, Sweden
3School of Life Sciences, CBS, University of Nottingham, NG7 2RD Nottingham, UK
4Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
5Structural and Molecular Microbiology, VIB Department of Structural Biology, VIB, 1050 Brussels, Belgium
6Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
7Department of Pathology, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
8Department of Chemistry, Umea University, 901 87 Umea, Sweden
9Max von Pettenkofer Institute of Hygiene and Medical Microbiology, LMU Munich, 80336 Munich, Germany
10Department of Medical Biosciences, Umea University, 901 85 Umea, Sweden
11Department of Odontology, Umea University, 901 87 Umea, Sweden
12Department of Medicine, USUHS, Bethesda, MD 20814, USA
13Department of Pediatrics, USUHS, Bethesda, MD 20814, USA
14Department of Microbiology and Immunology, USUHS, Bethesda, MD 20814, USA
15Kings College London, Dental Institute, London SE1 9RT, UK
16Department of International Health, John Hopkins School of Public Health, Baltimore, MD 21205, USA
17Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education & Research,
376 Cell Host & Microbe 21, 376389, March 8, 2017 2017 Elsevier Inc.
Asish K. Mukhopadhyay,18 G. Balakrish Nair,19,40 Konstantinos S. Papadakos,20,41 Beatriz Martinez-Gonzalez,20
Dionyssios N. Sgouras,20 Lars Engstrand,21,42 Magnus Unemo,22 Dan Danielsson,22 Sebastian Suerbaum,9,23,24,30
Stefan Oscarson,25 Ludmilla A. Morozova-Roche,1 Anders Olofsson,1 Gerhard Grobner,8 Jan Holgersson,26
Anders Esberg,11 Nicklas Stromberg,11 Marene Landstrom,10 Angela M. Eldridge,27,43 Brett A. Chromy,27,44
Lori M. Hansen,28 Jay V. Solnick,28,29 Sara K. Linden,4 Rainer Haas,9,30 Andre Dubois,12,45 D. Scott Merrell,14
Staffan Schedin,2 Han Remaut,5,6 Anna Arnqvist,1 Douglas E. Berg,31 and Thomas Boren1,46,*
25Centre for Synthesis and Chemical Biology, School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
26Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, University of Gothenburg,
Sahlgrenska University Hospital, 413 45 Gothenburg, Sweden
27Department of Pathology and Laboratory Medicine, University of California Davis School of Medicine, Sacramento, CA 95817, USA
28Departments of Medical Microbiology and Immunology, Center for Comparative Medicine, University of California Davis, Davis,
CA 95616, USA
29California National Primate Research Center, University of California Davis School of Medicine, Davis, CA 95616, USA
30German Center for Infection Research (DZIF), Munich Site, 80336 Munich, Germany
31Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
32Co-first author
33Present address: Swedish Defence Research Agency, 906 21 Umea , Sweden
34Present address: Umea Core Facility Electron Microscopy (UCEM), Umea University, 90187 Umea, Sweden
35Present address: Acreo Swedish ICT AB Box 53071, 400 14 Gothenburg, Sweden
36Present address: Universite de Strasbourg, CNRS, UMR7177, Institut de Chimie, 1, 67070 Strasbourg, France
37Present address: Department of Medical Biosciences, Umea University, 901 85 Umea, Sweden
38Present address: The Biochemical Imaging Center Umea (BICU), Umea University, 901 87 Umea, Sweden
39Present address: Faculty of Science and Technology, Umea University, 901 87 Umea, Sweden
40Present address: Research Policy and Cooperation Unit, Communicable Diseases Department, World Health Organization,
Mahatma Gandhi Marg, Indraprastha Estate, New Delhi 110 002, India
41Present address: Department of Translational Medicine, The Wallenberg Laboratory, Lund University, 205 02 Malmo , Sweden
42Present address: Science for Life Laboratory, SE-17165, Solna, Sweden
43Present address: Genentech, 1000 New Horizons Way, Vacaville, CA 95688, USA
44Present address: Singulex, Inc. 1701 Harbor Bay Pkwy, Suite 200, Alameda, CA 94502, USA
45Deceased June 30, 2012
46Lead Contact
*Correspondence: thomas.boren@umu.se
http://dx.doi.org/10.1016/j.chom.2017.02.013
billions of people worldwide and is implicated in peptic ulcer escaping from the mucosal debris that is shed into the acidic
disease and gastric cancer (Peek and Blaser, 2002). H. pylori and bactericidal gastric lumen.
thrives in the gastric epithelium and in the 300 micron thick Here we show that BabA-mediated binding is acid sensitive
overlying mucus, a special niche that is hostile to nearly all other and responsive, but also fully reversible and restored by pH
microbes (Figure S1I). The mucus layer normally contains a pH neutralization. The acid sensitivity profiles change by mutation
gradient from pH 6 to pH 2 between the epithelial and luminal and recombination with babA-related sequences driven by
boundaries and is intrinsically unstable with mucus and epithelial adaptation to differences in acidity in gastric regions and also
cells continuously being shed into the lumen (Schreiber et al., in different individuals.
2004; Lee, 1985). H. pylori is partially protected from luminal
acidity by epithelial secretions of buffering bicarbonate and RESULTS
urea and the ammonia generated by its urease (Sachs et al.,
2003), by chemotaxis away from acidity (reviewed in Keilberg Acid Response and Reversal of Leb Binding
and Ottemann, 2016), and by tight adherence to mucosal glycan We found that attachment of H. pylori strain 17875/Leb to
receptors (Ilver et al., 1998; Aspholm-Hurtig et al., 2004) medi- human gastric mucosal epithelium was acid sensitive, with
ated by attachment proteins (adhesins) that are extraordinary 2- and 20-fold less binding at pH 4 and 2, respectively,
in being acid responsive, as detailed here. The best-studied compared to pH 6 (Figure 1A). Equivalent acid-sensitive binding
H. pylori adhesin is BabA, which mediates high-affinity bacterial was seen with human MUC5AC gastric mucin and a clinical
binding to ABO/Leb blood group antigens (Leb) that are abun- H. pylori isolate (Figure 1B). A quantitative dissociation assay
dant on gastric epithelial cells and mucins (Aspholm-Hurtig showed detachment of >85% of previously bound Leb within
et al., 2004; Linden et al., 2002). BabA binding affinities 30 s of a pH 6 to pH 2 shift (Figure 1C). Leb binding at equilib-
(Ka 1071012 M 1) are orders of magnitude greater than most rium showed 10-fold lower affinity at pH 4 than at pH 6 and a
carbohydrate-binding proteins (Aspholm-Hurtig et al., 2004; further 2,000-fold reduction at pH 2, i.e., >20,000-fold decrease
Imberty et al., 2005) and aid H. pyloris delivery of effector mole- in total affinity (Figure 1D). Four sets of experiments showed
cules that subvert host defenses (Ishijima et al., 2011) and are that acid inactivation of H. pylori binding is reversible. First,
necessary for H. pylori replication (Tan et al., 2009) and nutrient H. pylori was preincubated at several low pHs and then
acquisition (Kirschner and Blaser, 1995). However, if such bind- restored to pH 5 (which is optimal for its Leb binding). Greater
ing were unalterable, this would prevent the bacteria from than 95% of the binding activity was recovered after initial
100 100
12 scored (mean SD for n = 2).
affinity (Ka, M -1 )
11 (D) The 4 3 1011 M 1 affinity (Ka) at pH 6 showed
Leb binding
75 75
10x
10 log-fold reductions at pH 4, 3.3, 2.8, and 2.1
50 50 100x
9 (arrows), and these are shown with 95% confi-
1000x
25 25 8 dence intervals (CI).
10.000x
7 (E) The acid sensitivity profile, here denoted
0 0
2 3 4 5 6 0 30 1 2 2 3 4 5 6 pHgram (in black), was determined by a 1 hr in-
pH Time at pH 2 (min) pH cubation with 125I-Leb at pH from 6 to 2. The
dashed line shows when half of the Leb binding
E F G remained, i.e., 17875/Leb pH50 = 3.4. Recon-
H. pylori attachment (I)
80
Relative Leb binding (%)
incubation at RpH 3, and 87% and 74% after incubation at BabAs Polymorphic and Reversible Acid Sensitivity in
pH 2.5 and 2.0, respectively (in red, Figure 1E). Second, prior Binding
acidification did not affect Leb binding kinetics (Figure S1B). Acid sensitivity of 21 Swedish clinical isolates (SW) was scored
Third, 87% of Leb binding was retained after five full cycles as the pH at which half the maximal Leb binding was lost
of pH 2.5 acidification and pH 5 restoration (this is referred to (pH50). The pH50 values ranged from 2.3 (the most acid resistant)
as a pH-cycle) (Figure 1F). Fourth, H. pylori were applied to a to 4.9 (the most acid sensitive) (Figure 2A) (median = 3.7; Fig-
LigandTracer dish (Figures S1CS1H) coated with Leb-ex- ure 6F). Thus, acid-sensitive Leb binding is a general trait but
pressing buccal epithelial cells (BECs), collected from a Leb- with differences among strains, which suggests that H. pylori
expressing volunteer that represent an authentic epithelial can adapt to individual acid secretion patterns. To test in real
glycosylation pattern typical of human primary gastro-intestinal time for adaptation by selection and gain of function, bacterial
epithelium (Figure 1H) or with Leb-expressing recombinant cells of the acid-resistant strain SW7 and the more acid-sensitive
CHO cells (Figure S1G), and attachment was LigandTraced strain SW38 (Figure 2A) were mixed and exposed to a pH-cycle
to monitor bacterial binding as a function of pH in real time. and LigandTraced. The two strains attached most similarly to the
Attachment to both cell types was again lost at pH 2 and re- Leb-coated dish at neutral pH, but after stepwise acidification to
gained at pH 6 (Figures S1H and 1G), though the response to pH 3, followed by reconditioning to pH 6, the SW7 strain had a
acidification was more pronounced with Leb-CHO cells that 2-fold increase in binding compared to SW38 (Figures 2B
overexpress the Leb antigen compared to the authentic and and S2C).
more complex BECs. Seven experiments tested if reversible acid sensitivity and
These results inspired our dynamic model in which H. pylori pH50 differences among strains stem from differences in BabA
bacteria escape from shed mucosal debris as they move toward protein sequence. First, a Far-Western test showed that Leb
the acidic and bactericidal lumen and then return to the epithelial binding to size-separated BabA protein was maximal at
surface and proximal mucus through chemotaxis where the bac- pH 56 and negligible at <pH 3 (Figure 2C). Second, immuno-
teria with best adapted ability in adherence reattach to their Leb blotting showed that the BabA protein was stable at pH 2 for
binding sites (Movie S1). 24 hr (Figure S2D). Third, a babA deletion mutant of strain
SW7
400
75
*** terms to facilitate inter-strain comparison in acid
sensitivity in binding (absolute Leb binding is
300
shown in Figure S2A). Each individual pHgram and
50 pH50 value is highly reproducible (Figure S2B).
200 (B) Attachment at pH 6 and re-attachment after a
25
full pH-cycle (Figure S2C, similar to Figure 1G) by
SW7 100 strains SW7 (Alexa555, red) and SW38 (Alexa488,
SW38 green) were significantly different as measured
0 0 by Bonferroni post hoc tests (mean SD, n = 7
2 3 4 5 6 pH 6 pH 6
and n = 10 field views for SW7 and SW38,
pH recovered
respectively).
C D E
Leb (C) 17875/Leb whole-cell proteins were separated
kDa a b
100 by SDS-PAGE, transferred to a membrane, and
strips were probed with Leb (Ilver et al., 1998) at
Relative Leb binding (%)
250 -
Relative Leb binding (%)
SW38 (pH50 = 3.8) was transformed with babA from acid-resis- local shifts in native BabA protein secondary and tertiary struc-
tant SW7 (pH50 = 2.4). The transformant with SW7s complete ture (Figure S2J). Seventh, for comparison, the common blood
babA gene, Trans38-7, had a pH50 of 2.8 and thus had group O antigen binding lectins UEA and AAA were tested, and
gained 75% of SW7s acid resistance (Figure 2D). Fourth, unlike BabA, acid inactivation was found to be irreversible for
native 17875/Leb BabA protein purified to homogeneity (Figures both lectins (Figure S2K). Thus, the BabA protein sequence
2E, S2G, and S2H) bound specifically to human gastric foveolar determines acid sensitivity in Leb binding, its remarkable
epithelium at pH 6 (Figure 2Fa). Acidification to pH 4 and pH 2 reversibility, and the diversity of sensitivity among strains.
caused 15% and >99% detachment, respectively (Figures
2Fb, 2Fc, and S2I), with binding at pH 6 being unaffected by prior Gastric Antrum-Corpus Differences in Acid Sensitivity in
incubation at pH 2 (Figure 2Fd). Fifth, BabA purified from strains Binding
SW7, 17875/Leb, and SW38 showed pH50 values with the same The gastric antrum is less acidic and has a thicker protective
rank order as those of their source bacteria, although with acid mucus layer than the gastric corpus, which contains the acid-
sensitivities 0.9, 0.2, and 0.3 pH units higher, respectively (Fig- producing parietal cells (Figure S3A). To assess if regional gastric
ure 2G). Sixth, circular dichroism (CD) spectra showed that physiology might select for pH50 differences in resident H. pylori
acidification from pH 7 to pH 4 and pH 2.5 caused only minor strains, we studied 20 antrum and 10 corpus isolates from
75 40
denoted as Key-position. This is the first residue in a short
50 a-helix (amino acids 199202) called the Key-coil because it
PG
20
affects the acid sensitivity in Leb binding (Figures 4A, 4B, and
PE
25 S4A). Replacement of P199 with L can turn Key-coil into a
LE
LG
random coil (Krieger et al., 2005). Similar L to P substitutions
0 0 with subsequent structural alterations are recognized human
3 4 5 6 PG PE LG LE Ctrl
pH cancer markers (Kundu et al., 2013). We also found that 5 of
the 30 SO-2 isolates were exceptional in having an antrum-
Figure 3. Gastric Antrum versus Corpus Adaptation in Acid Sensi- like median pH50 of 4.4 (Figures 3A and 3B) but corpus-like
tivity and Affinity in Binding Is Encoded in BabA affinities 20-fold and 50-fold higher than other antrum isolates
(A) pHgrams of 30 isolates from patient SO-2 from Orebro University Hospital, at pH 6 and pH 4, respectively (Figure S3E). This unusual pH50
Sweden. The most and least acid sensitive isolates displayed a full pH unit and affinity combination revealed a corpus-like P199 paired
difference.
with E192K and G205D substitutions. Positions 192 and 205
(B) The Exceptional Antrum (AEx) and Corpus (CEx) isolates are circled.
(C) Location of the SO-2 BabA substitutions: P199L in Key-position and are both located next to the Key-position in BabAs carbohydrate
E192K/G205D in the Exceptional (Ex) isolates are all in the proximity of the binding domain (CBD) (Figure 4B). The second set of substitu-
fucose-binding CL2 disulfide-clasped loop (yellow) that constitutes the basis tions that influence the acid sensitivity of SO-2 BabA is G/E428
for the CBD. The G428E substitution is located diametrically opposite the CBD in Helix-9 (H9), which is located 40 A away from the CBD.
where it is part of Velcro Domain and is situated at the very junction of the H9, together with H1 and H10, form a coiled-coil Stalk Domain
Repeat-Sequence-1, i.e., the C-terminal 300 amino acid segment including the
connecting BabAs surface-exposed domains and membrane-
membrane anchored domain (Figure 4B) that is conserved between BabA,
BabB, and BabC (Alm et al., 2000).
anchored domains (Figure 4B) (Hage et al., 2015). We denote
(D) SPR-derived pHgram analyses of Leb-binding by E. coli recBabA526 pro- this trio of helices as BabAs Velcro Domain (Figure 4B). We
tein from SO-2 corpus (P199/G428, PG), antrum (L199/E428, LE), and chimeric suggest that the Velcro Domain contributes to BabA multimeri-
variants L199/G428 (LG) and P199/E428 (PE) (sensograms in Figure S3C). zation and thus to its binding avidity (Figures 6 and 7).
(E) Leb binding by E. coli bacterial cells that express full-length recBabA720 BabA differences that reflect adaptations to local gastric
from SO-2 corpus (PG), antrum (LE), and chimeric variants LG and PE was
sites were also seen in the analysis of 30 Greek isolates that,
assessed by RIA. E. coli with no expression of recBabA was used as the
control (Ctrl) (mean + SD for n = 2).
similar to the Swedish isolates, exhibited a range of pH50 values
from 3.3 to 5.3 (Figure S4Ba), with a median pH50 of 3.8 (Fig-
ure 6F). Of the 13 strains that demonstrated Leb binding in
Swedish patient SO-2 with reflux dyspepsia. These isolates had both antrum and corpus isolates, four strains exhibited pH50
a median difference of 0.7 pH units (pH50 4.4 in the antrum and antrum-corpus differences, from +0.9 to 0.6 pH units. The
3.7 in the corpus, Mann-Whitney U test, p < 0.0001) (Figure 3A). antrum isolates from two patients (G0017 and G1055) were
All SO-2 isolates had identical glr and cysS housekeeping gene more acid sensitive, whereas the corpus isolates from two
sequences (Table S5), indicating recent descent from the same other patients (G1034 and G2030) were more acid sensitive
ancestral strain. In contrast, no significant pH50 differences (Figure S4BbS4Bf). For comparison, an equivalent difference
were found among isolates from another patient, SO-1, with in acid-sensitive Leb binding of the G1007 antrum versus
corpus isolates was seen with human MUC5AC gastric mucin BabA-Leb interactions (through the CBD) and monomer-olig-
(Figure S4C). The antrum and corpus isolate pairs differed by omer transitions (through the Velcro Domain).
379 amino acid substitutions (Figure S4D), and each isolate
pair had identical glr and cysS housekeeping gene sequences BabA Acid Sensitivity and Geographic Disease Patterns
(Table S5). These substitutions tightly overlap the BabA The babA genes are far more diverse than other H. pylori genes,
Clusters IIII, i.e., domains that are high in positive-selection as illustrated by the unique sequences of 100 full-length BabAs
activity (with amino acid substitution as a consequence of (Figure S5A), and this diversity is shaped by multiple selective
nucleotide mutation), including the CBD (Figure 4A). Also pre- forces, including ABO blood group phenotypes and differences
sent are three amino acid substitutions in the Velcro Domain in the gastric physiology among human populations. Because
of strain G1007, including E428G (Figure S4D), which is iden- H. pylori infection is associated with pangastritis, corpus atro-
tical to the Velcro Domain substitution in patient SO-2 (Fig- phy, hypochlorhydria (higher gastric pH), and elevated gastric
ure 3C). The positions of these substitutions suggest that cancer risk in Peru (Correa, 2013) versus antrum-predominant
they have direct acid-responsive effects on both monomeric gastritis (Misra et al., 2000), hyperchlorhydria (lower gastric
100
3.16 I18 TCSGEGNDNC SKQAT GV----ENQ
QSGGTKTETQTIDGKSVN
3.48 I110 TCSGEGNDNC SRQAT GV----NNQ
QNGGTKTETQTIDGKTVN
3.87 I21 TCSGEGNNNC D--AL -----KNNRNGGSKTETQTIGGKSVN
3.96 I120 TCSGDGNDNC T--IT GL----EQQ
QNG-SKTETQTIDGKTVT
4.05 I93 Ex TCSGK
KGNNNC D--AL G----D
DK-RNGGTKTETQTIDGKQVN
Relative Leb binding (%)
75
4.10 I78 TCSGKGNNNC D--VL -----KNNRNGGTKEETQTIDGKQVN
4.13 I60 TCSGEGNNNC Q--IT GL----K-Q
QRGGTKTETQTIDGKSVN
4.17 I9 Ex TCSGK
KGNNNC D--VL -----KD
DNRNGGTKTETQTIDGKSVT
50 4.18 I17 Ex TCSGK
KGNNNC D--VL -----KD
DNRNGGTKTETQTIDGKSVT
4.21 I109 TCSGEGNDNC T--IT DV---KR-RNG-TKTETQTIDGKSVT
Peru 4.27 I119 TCSGEGNNNC D--AL KD-ALKDNRNGGTKTETQTIDGKSVN
4.37 I102 TCSGEGNNNC E---- -----DHSR---TKTETQTIDGKSVS
India
25 4.50 I99 TCSGGGNNNC T--IT GL----KQQ
QNG-TKTETKTIDGKSVS
I18wt
3.66 J532 TCSGEGNDNC SPRVT GV----DKQ
QDGGNKTETKTIDGKQVT
P
I9wt 3.74 J519 TCSGEGNDNC SPSVT GV----TNQ
QSNGTKTETQIIDGKTVN
0 4.21 J511 TCSGENNNNC S--IT GV----RQQ
QNG-TKTETQTIDGKSVS
2 3 4 5 6 4.40 J512 TCSGEGNNNC T--IT GV----KQQ
QNG-YKTETKTIDGKQVT
P
pH
4.12
P
S851 TCSGEGNNNC T--IT GV----NNQ
QNGGTKTTTQTIDGKSVN
Key-position
PLPPK
C D E F
CD - - VL - - K - DNRNGG
P
I9 100
KK I
M3 M1
50
CSKQATGV - - ENQSGG 50
Q
I18
I M2 I18-SV
EI
199 207 25 25
A BabA Repeat Sequence
M3 I18-SV- KQ
0 0
EQ S
1 240 480 720 2 3 4 5 6 2 3 4 5 6
pH pH
CBD-domain
G H I
100
I9-SV Loading rate [pN/s]
E
10
Thermal off-rate [s -1 ]
Relative binding (%)
50 2700
Bond strength [pN]
75 I9-SV-D198A
T KL
1
40 480
YTH
68
K 50 30 0.1
Q 20 6.8
25 0.01
Sweden
Greece
Alaska
10
Japan
Spain
India
Peru
0 0 0.001
2 3 4 5 6 3 4 5 6 7 3 4 5 6 7
pH pH pH
Figure 5. Acid Inactivation of Leb Binding Depends on the pH Response-Sensor in the Key-Coil
(A) pHgrams of 17 Asian Indian and 20 Peruvian strains with acid-resistant Indian I18 shown in red and more acid-sensitive Indian I9 shown in green.
(B) BabA sequences from 17875/Leb, the Asian-Indian strains (I), and strains from Japan (J) and Spain (S) with/without Key-coil positions 199 and 200 ranked
according to their pH50. A red vertical box indicates the Key-coil. The acid-resistant strain I18 (horizontal red box) and acid-sensitive strain I9 (horizontal green
box) are indicated. The three green arrows show strains that carry the K192/D205 Exceptional (Ex) motif for increased acid sensitivity in binding (similar to Ex motif
in Figure 3C).
(C) The prevalence of P in the Key-position is 25% in Europe, 50% among North American Amerindians (Alaska), and 90% among South American
Amerindians (Peru) (Table S2). The red vertical box illustrates the missing Key-position in most Indian strains.
(D) The three I9-SV BabA mutants (M) with 3, 8, or 11 amino acids from the Key-coil region of strain I18.
(E) pHgrams show that BabA I9 with the S198S208 (11 aa) segment, expressed in H. pylori strain P1DbabA, gave strain M3 a 60% increase in acid resistance
(arrow) compared to the original I9 strain (pH50 4.17). M3 pH50 = 3.56 (blue), whereas the M1 and M2 mutants (orange) showed contrasting increased acid
sensitivity (pH50 = 4.46) (mean SD for n = 5 [M1], n = 6 [M2 and M3], or n = 3 [I9 and I18] individual clones).
(F) Recombinant expression of BabA I18-SV and I18-SV-DKQ in H. pylori strain P1DbabA demonstrated increased acid sensitivity from pH50 3.3 to 3.9 (mean SD
for n = 4) due to deletion of the two residues 199K and 200Q.
(G) Recombinant expression of BabA I9-SV and I9-SV-D198A in H. pylori strain P1DbabA demonstrated increased acid sensitivity from pH50 = 4.1 to 4.9 (mean
SD for n = 4) due to inactivation of the salt bridges D-node by the D198A substitution.
(H) Bond strengths for twelve combinations of acidity and loading rate. These are the effective loading rates for the binding when the influence of the elasticity of
the bacterium body has been compensated for (Bell, 1978).
(I) The off-rate was assessed by a linear fit of the measured bond strength versus the logarithm of the loading rate (from H), where the off-rate is calculated from the
slope of this line (Bjornham et al., 2009). The measured increase in off-rate (dissociation) is comparable to the decrease in bacterial binding affinity at pH 3.6
(Figure 1D). The results are based on >4,000 single measurements.
K a, M -1
81G C BabB QE A E K S S
pH 50
S D S A
RA
E
450
E
G
S E
454
AD L Y A H K
469
N K
475
S S V I
KV
SI
N
486
G S A I S
V
A G Q
(Figure S6G).
(C) UniProt alignment of 98 BabA Velcro Domain
sequences with the seven 81G substitutions
indicated.
Helix 9 Helix 10 (D) pHgrams of H. pylori isolated from the GC-
D E Key-position
patient at year 0 (Y0), Y3, Y16-1, Y16-2, and Y16-3
(mean SD, n = 2).
Relative Leb binding (%)
100 Y16-3 Y0, Y3 IN D C R T CD PSVT -ANN- N TG T (E) BabA alignment of the Y0/Y3 (identical) iso-
Y16-2 Y16-1 IN D C G T CNPSLF IANNE G TK T
75
lates, the Y16-1 isolate, and the more acid-sen-
Y16-2/3 VS T C G N CSPKVT -VDK- G ST I
Y16-1 sitive Y16-2/3 (identical) isolates, where all but one
180 190 200 210
50 Y3 Y0, Y3
substitution (aa343) are located in the CBD (in red,
G Q N D T LH N S
Y16-1 G Q N D T LH N S blue, and green, respectively; see D).
25 Y0 Y16-2/3 D R T N N SR E N (F) Boxplots of pH50 for 26 SO-1 (non-reflux
220 230 240 250 dyspepsia) isolates, 20 SO-2 (gastric reflux) antrum
0
2 3 4 5 6 Carbohydrate Binding Domain (A) and 10 SO-2 corpus (C) isolates (Figure 3A), and
pH Year 0,3 21 Swedish (Figure 2A), 30 Greek (Figure S4B), 17
Year 16-1 Repeat Sequence-1 Indian, and 20 Peruvian (Figure 5A) strains with
Year 16-2/3 values outside the box shown as individual points.
1 120 240 360 480 600 720
Mann-Whitney U tests show significant differences
F G (**p < 0.01; ***p < 0.001).
6 80 (G) Tests of strains from Sweden (n = 21), Peru
*** ** Sweden
(n = 20), India (n = 17), Greece (n = 30), and Japan
Greece (n = 22) showed that acid sensitivity (pH50) cor-
pH at 50% binding
5 60
Leb binding (%)
2 0
2 3 4 teins adapted due to recombinational
5
A
-1
en
ru
ec
di
SO
-2
-2
Pe
pH50
ed
SO
Sw
(Figure 6D), although all isolates were similar in binding capacity trophoresis showed that BabA proteins migrate as oligomeric
and affinity (Figure S6H). Again, the identical glr and cysS gene and high molecular mass (HMM) multimeric complexes (Figures
sequences in the isolates verify that they derived from the 7A, 7B, and S7A). Second, BabA eluted as oligomeric complexes
same ancestral strain (Table S5). The BabA sequences from Y0 during cation exchange (CEX) chromatography (Figure 7C).
and Y3 were identical and differed from Y16-1 by 9 substitutions Third, the bacterial whole-cell protein level of BabA (Table S1)
and from Y16-2 and Y16-3 by 25 substitutions (Figure 6E; Table compared to bacterial cell Leb-binding capacity (Figure 1D)
S5). All but one of these acid sensitivity-determining amino acid gave a ratio of 2.8 BabA proteins per binding site, which sug-
substitutions stem from single nucleotide differences, cluster in gests that the high-affinity form of BabA is a trimer. Fourth, in
the CBD (yellow segment in Figure 4A), and are specifically contrast to the acid stability of the native BabA protein, CD
located in intrinsically unstructured regions (green bars in Fig- spectra of the 81G antrum and corpus recBabA526 fragments
ure 4A) where they can modulate the reactivity of these loops. show structural transitions at pH 4.5, which suggests that the
The dual clustering of apparently adaptive BabA substitutions C-terminal b-barrel membrane domain and proximal Velcro
in the CBD and Velcro Domain during chronic infection and pro- and Stalk domains indeed contribute to structural support (Fig-
gression to gastric cancer illustrates the importance of these two ure S2J versus S7B). Fifth, small-angle X-ray scattering (SAXS)
domains in determining BabAs acid sensitivity and Leb affinity. showed recBabA in pure monomer form below pH 4, whereas
BabA forms discrete higher molecular weight species above
Acid Sensitive and Reversible BabA Multimerization pH 6 (Figure S7C). Sixth, non-reducing (less denaturing) SDS-
We investigated whether BabAs reciprocity in acid sensitivity PAGE showed that BabA released from H. pylori membranes
versus high affinity in Leb binding depends on the CBDs intrinsic by the mild detergent ZW-12 is oligomeric but is monomerized
affinity seen in BabA monomers combined with multimeric avid- by acidification to <pH 4 (Figure 7D). Seventh, crosslinker treat-
ity in binding through Velcro Domain interactions. First, 2D-elec- ment of H. pylori bacterial cells at different pHs identified BabA in
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ACKNOWLEDGMENTS Science 279, 373377.
Imberty, A., Mitchell, E.P., and Wimmerova, M. (2005). Structural basis of high-
This paper is dedicated to the memory of our friend, collaborator, and co-
affinity glycan recognition by bacterial and fungal lectins. Curr. Opin. Struct.
author Dr. Andre Dubois, a great scientist who contributed importantly
Biol. 15, 525534.
both intellectually and materially to this project. We thank S. Michopoulos
Ishijima, N., Suzuki, M., Ashida, H., Ichikawa, Y., Kanegae, Y., Saito, I., Boren,
and G. Mantzaris for H. pylori clinical isolates and O. Furberg (NoPolo.se),
T., Haas, R., Sasakawa, C., and Mimuro, H. (2011). BabA-mediated adherence
N. Ulander (softplanbangkok.com), S. Lindstrom, and M. Boren for the digital
is a potentiator of the Helicobacter pylori type IV secretion system activity.
movie, tech, art, and figure work, respectively. This work was supported by
J. Biol. Chem. 286, 2525625264.
grants from Vetenskapsradet (VR/M) to T.B. and S.K.L., Cancerfonden to
T.B. and A.A., VR/NT to A.A. and S. Schedin, Formas to S.K.L., the J.C. Keilberg, D., and Ottemann, K.M. (2016). How Helicobacter pylori senses, tar-
Kempe and Seth M. Kempe Memorial Foundation, the Knut and Alice Wal- gets and interacts with the gastric epithelium. Environ. Microbiol. 18, 791806.
lenberg Foundation (2012.0090) to T.B. and M.L., European Union Seventh Kennemann, L., Didelot, X., Aebischer, T., Kuhn, S., Drescher, B., Droege, M.,
Framework Program GastricGlycoExplorer ITN grant number 316929 to Reinhardt, R., Correa, P., Meyer, T.F., Josenhans, C., et al. (2011).
T.B. and Y.A.C., Magn. Bergvalls Foundation to S. Schedin, DFG (SFB Helicobacter pylori genome evolution during human infection. Proc. Natl.
900/A1) to S. Suerbaum, DFG (HA2697/16-1) to R.H., FP6 ANR-06-PATHO- Acad. Sci. USA 108, 50335038.
00701 ERA-NET and Actions Concertees Inter-Pasteuriennes (ACIP) (2006) Kirschner, D.E., and Blaser, M.J. (1995). The dynamics of Helicobacter pylori
to D.N.S., NIH R01DK063041 to D.E.B., NIH CA082312 to D.S.M., NIH infection of the human stomach. J. Theor. Biol. 176, 281290.
AI070803 and AI081037 to J.V.S., CSIR project, India (No. 37(1640)/14/
Krieger, F., Moglich, A., and Kiefhaber, T. (2005). Effect of proline and glycine
EMR II) to A.K.M., and VIB and FWO (grants: G033717N and 12H8416N)
residues on dynamics and barriers of loop formation in polypeptide chains.
to K.M. and H.R. This work was in part performed within the Umea Centre
J. Am. Chem. Soc. 127, 33463352.
for Chronic Infectious Disease (UCCID), Umea Centre for Microbial Research
(UCMR), and the Biochemical Imaging Centre Umea (BICU) within the Na- Kuipers, E.J., Lundell, L., Klinkenberg-Knol, E.C., Havu, N., Festen, H.P.,
tional Microscopy Infrastructure (NMI). T.B. is a founder of Helicure and a Liedman, B., Lamers, C.B., Jansen, J.B., Dalenback, J., Snel, P., et al.
member of its scientific advisory board. (1996). Atrophic gastritis and Helicobacter pylori infection in patients with re-
flux esophagitis treated with omeprazole or fundoplication. N. Engl. J. Med.
Received: August 24, 2016 334, 10181022.
Revised: December 16, 2016 Kundu, A., Bag, S., Ramaiah, S., and Anbarasu, A. (2013). Leucine to proline
Accepted: February 17, 2017 substitution by SNP at position 197 in Caspase-9 gene expression leads to
Published: March 8, 2017 neuroblastoma: a bioinformatics analysis. 3 Biotech. 3, 225234.