Received 23 Jul 2015 |Accepted 12 Oct 2015 |Published 2 Dec 2015
Ankyrin-mediated self-protection during
cell invasion by the bacterial predator
Carey Lambert1,*, Ian T. Cadby2,*, Rob Till1, Nhat Khai Bui3, Thomas R. Lerner1,w, William S. Hughes2,
David J. Lee2, Luke J. Alderwick2, Waldemar Vollmer3, R. Elizabeth Sockett1& Andrew L. Lovering2
Predatory Bdellovibrio bacteriovorus are natural antimicrobial organisms, killing other bacteria
by whole-cell invasion. Self-protection against prey-metabolizing enzymes is important
for the evolution of predation. Initial prey entry involves the predator’s peptidoglycan
DD-endopeptidases, which decrosslink cell walls and prevent wasteful entry by a second
predator. Here we identify and characterize a self-protection protein from B. bacteriovorus,
Bd3460, which displays an ankyrin-based fold common to intracellular pathogens of
eukaryotes. Co-crystal structures reveal Bd3460 complexation of dual targets, binding a
conserved epitope of each of the Bd3459 and Bd0816 endopeptidases. Complexation inhibits
endopeptidase activity and cell wall decrosslinking in vitro. Self-protection is vital — DBd3460
Bdellovibrio deleteriously decrosslink self-peptidoglycan upon invasion, adopt a round mor-
phology, and lose predatory capacity and cellular integrity. Our analysis provides the ﬁrst
mechanistic examination of self-protection in Bdellovibrio, documents protection-multiplicity
for products of two different genomic loci, and reveals an important evolutionary adaptation
to an invasive predatory bacterial lifestyle.
DOI: 10.1038/ncomms9884 OPEN
1Centre for Genetics and Genomics, School of Biology, Nottingham University, Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, UK.
2Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK. 3Centre for Bacterial Cell Biology,
Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK. wPresent address: Francis Crick
Institute, London NW1 2BE, UK. * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to R.E.S.
(email: email@example.com) or to A.L.L. (email: firstname.lastname@example.org).
NATURE COMMUNICATIONS | 6:8884 | DOI: 10.1038/ncomms9884 | www.nature.com/naturecommunications 1
Bdellovibrio are deltaproteobacteria that enter and kill
diverse pathogenic Gram-negative bacterial species and
have been tested as possible whole-cell antibacterial
agents1,2.Bdellovibrio bacteriovorus is a periplasmic predator
that enters through the outer membrane of prey and metabolizes
the ‘infected’ cell from within3. The intracellular lifestyle of
B. bacteriovorus requires many specialized adaptations4, one of
which is the formation of the osmotically-stable bdelloplast,
wherein the (usually) rod-shaped prey cell becomes rounded up
immediately after Bdellovibrio instigates prey invasion5. This
rounding is caused by prey peptidoglycan cell wall modiﬁcation,
catalysed by Bdellovibrio enzymes6. The B. bacteriovorus genome
encodes many predation-associated genes, additional to those for
self cell wall maintenance. These gene products modify prey
peptidoglycan in sequential, but different, ways to facilitate
bdelloplast formation: withstanding initial predator-invasion
without breaking; accommodating the invasive Bdellovibrio
growing within; withstanding and becoming ready for ﬁnal lysis
when Bdellovibrio replication is complete. Although these cell
cycle concepts and associated cell wall modiﬁcations are predicted
and seen microscopically as events, few activities have
been directly attributed to speciﬁc Bdellovibrio predatory gene
products. Previously, we assigned prey cell rounding to the action
of two secreted Bdellovibrio peptidoglycan DD-endopeptidases,
Bd0816 and Bd3459, that act to modify the invaded cell wall via
hydrolysis of the structural 3-4 peptide crosslinks6. The prey
morphology-change catalysed by these enzymes functioned as an
‘occupancy signal’, preventing wasteful entry by successive
predators and speeding up prey invasion6. Thus, rounded prey-
bdelloplast formation, catalysed by the pair of DD-endopeptidase
enzymes (Bd3459, Bd0816) was found to promote a 1:1 predator
to prey cell ratio and drive population ﬁtness, preventing
self-competition between individual Bdellovibrio for the same
prey cell. This feature is important as although the long range
encounter between predator Bdellovibrio and a cloud of potential
prey involves chemotaxis7; the ﬁnal short range encounter cannot
be guided by chemotaxis as bacteria do not sense chemotactically
along their cell bodies at short range8. Thus, several Bdellovibrio
will arrive at a single prey cell as they cannot use self or prey
sensing to prevent this. Furthermore, Bdellovibrio are released as
a cloud of predators by lysis of an adjacent infected bdelloplast.
However, the ‘occupancy signal’ of DD-endopeptidase-mediated
rounding does prevent multiple entry to a single prey cell. Thus
these DD-endopeptidase enzymes are vital to predation efﬁciency
but they also target peptidoglycan, which is common to both
predator and prey; the evolutionary ﬁtness beneﬁt of eliminating
auto-competition brings with it a risk of self-damage which must
Structure and activity analyses of DD-endopeptidase Bd3459
revealed a highly active enzyme with an open active site adapted
for prey peptidoglycan diversity, rather than self-wall main-
tenance (this was also inferred for the homologous Bd0816). This
raised the intriguing question of how Bdellovibrio protects its own
cell wall from modiﬁcation/destruction by Bd3459 and Bd0816
passing through its own periplasm when invading prey6. To this
end, we instigated a search to ﬁnd a potential ‘self-protection
protein’ that could act to block endopeptidase activity in the
predator, while such DD-endopeptidases were being secreted,
past their own peptidoglycan cell wall to that of the prey.
Here we show that Bdellovibrio bacteriovorus utilizes a
small ankyrin repeat protein, Bd3460, to protect itself from
endopeptidase activities during entry of prey. We demonstrate
that endopeptidase complexation by Bd3460 prevents cell wall
decrosslinking, and that both the Bd0816 and Bd3459 targets
bind this self-protection protein via a common epitope. Predators
lacking this protection are observed to deleteriously self-round
upon cell contact and endopeptidase induction; thus forming an
abortive ‘spheroplast-like shape’ at the entry pore and negating
prey cell entry & killing.
Characterization of a Bdellovibrio self-protection protein.
Reasoning that protective protein(s) should act on both
DD-endopeptidase gene products in the periplasm, we examined
the gene neighbourhoods of bd0816 and of bd3460 initially
looking for a common pair of potential ‘immunity genes’, which
we didn’t ﬁnd. Gene bd0816 is preceded by a small 150 bp gene
without a signal peptide; bd3460 however encodes a small 23 kDa
protein, with predicted ankyrin repeats on a signal peptide.
Ankyrin-repeat proteins (ARPs) are often involved in protein-
protein interactions and can be found in several toxins and their
associated immunity proteins9,10. Interestingly, ARPs are rare in
bacteria, but are enriched in intracellular parasites of eukaryotes
where they are chieﬂy used to modulate host cell processes11.
The bd3459 endopeptidase/bd3460 ARP gene synteny, albeit with
ARP expressed after the protein it should protect against
(see explanation later), is shared in other periplasmic predator
genomes12, and is absent in related strains exhibiting epibiotic
predation (which adhere to prey but do not invade13). This
cumulative evidence suggested that Bd3460 could represent the
ﬁrst self-protection protein identiﬁed in predatory bacteria, a
hypothesis we test and validate in the present study.
Co-transcription of bd3459 and bd3460 was established via
semi-quantitative RT-PCR (Supplementary Fig. 1, showing peak
expression at prey invasion timepoints). Co-puriﬁcation of tagged
Bd3459/Bd0816 and untagged Bd3460 indicated a 1:1 complex
formation in-vitro. These interactions were conﬁrmed and
quantiﬁed using intrinsic tryptophan ﬂuorescence emission
measurements (Supplementary Fig. 2); with an estimated
afﬁnity of Bd3460 for Bd3459 of 26.8 uM. Acylation of the
DD-endopeptidase active site serine by the speciﬁc inhibitor
penicillin G caused an approximate 2-fold reduction in afﬁnity of
Bd3460 for Bd3459.
We utilized an identical assay to our original Bd3459
characterization6, wherein isolated peptidoglycan from a
pentapeptide-rich strain of Esherichia coli is incubated with
enzyme and modiﬁcations are monitored via endpoint HPLC
analyses. Puriﬁed recombinant Bd3460 completely inhibited the
endopeptidase activity of Bd3459, as expected for a functional
immunity protein (Supplementary Fig. 3).
Gene bd3460 lies downstream of bd3459 raising the questions:
how does it protect the cell when bd3459 is transcribed, and
translated before it; and how may Bd3460 protect against Bd0816
transcribed and translated from a gene locus elsewhere on
the genome? Monitoring ﬂuorescence of Bd3460::mCherry
throughout the predatory cycle showed that Bd3460 is expressed
in pre-invasive Bdellovibrio (Fig. 1), and expression increased
slightly during Bdellovibrio prey-entry and rounding (at the time
that Bd3459 and Bd0816 are utilized to effect prey cell wall
decrosslinking). Released, daughter attack-phase Bdellovibrio
maintained Bd3460::mCherry ﬂuorescence, indicating that
constant Bd3460 availability is the mechanism by which the
Bdellovibrio cell is protected from the upstream, earlier expressed
Bd3459 and Bd0816 upon the next prey encounter and invasion.
Prey-expression of Bd3460 protects against decrosslinking.
That Bd3460 does antagonize Bd3459 activity in an intracellular
niche was shown by the observation that expression of Bd3460 in
E. coli prey signiﬁcantly reduced the rounding of prey when
attacked by wild-type Bdellovibrio (Fig. 2a). This effect was
also seen for mutant Bdellovibrio with single deletions of either
ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9884
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bd0816 or bd3459, providing evidence that activity of both DD-
endopeptidases is antagonized by Bd3460.
High-level expression of Bd3459 from a vector with a tightly
controlled promoter in E. coli cells has previously been shown to
induce bacterial lysis6, with cells rounding up, swelling and ﬁnally
bursting. Simultaneous co-expression of Bd3460 resulted in
signiﬁcant protection from the lytic effect of Bd3459 induction,
with a larger proportion of E. coli cells remaining rod-shaped and
growing by binary ﬁssion. That a proportion of the cells were still
deformed and lysed shows that there was an imbalance of the two
interacting species which led to active unbound Bd3459 protein
damaging the cells (Supplementary Fig. 4).
Predator Dbd3460 mutants self-round upon prey recognition.
Attempts to delete bd3460 in predatory Bdellovibrio cells14, grown
on prey, yielded only wild-type revertants or merodiploid strains.
However bd3460 deletions were readily obtained in HI
(host/prey—independent) Bdellovibrio cells grown on artiﬁcial
media without prey present. As Bdellovibrio does not prey on
itself, there is no induction, under HI conditions, of Bd3459/
Bd0816, thus the absence of Bd3460 was not detrimental in these
circumstances. The HI strain with the bd3460 deletion was then
offered prey (HI Bdellovibrio do retain predatory abilities14). For
wild-type Bdellovibrio this leads to prey binding, recognition and
invasion (Fig. 3a). However, for the Bd3460 mutant there was a
period of prey-binding and then after 41.5±26.5 min of
attachment the Bdellovibrio cell suddenly (within 3.3±1.4 min)
rounded up (example in Fig. 3b). Thus the Bd3459/Bd0816
DD-endopeptidase enzymes acted upon the self-cell wall of the
Bdellovibrio Dbd3460 mutant. These enzymes were still secreted
from the Dbd3460 mutant into the prey as evidenced by prey
rounding (Fig. 3b). In addition, other damage was observed, such
as leakage of the prey cell contents at the point of Bdellovibrio
contact (Supplementary Fig. 5). This suggests that the predator
was still breaching the prey outer membrane, but was unable to
enter due to its own rounded deformation. The expression of
either Bd0816 or Bd3459 from the Bdellovibrio was sufﬁcient to
cause predator self-rounding in the absence of Bd3460. Double
mutants of Bd3460/Bd3459 and Bd3460/Bd0816 could only be
isolated as host-independent isolates and also rounded up upon
contact with prey cells (Supplementary Fig. 6). Triple mutants of
bd3460/bd3459/bd0816 were readily obtained and were capable of
prey entry similar to wild-type in lab conditions (Supplementary
Fig. 6). These observations ﬁt with electron micrographs of prey
entry, wherein wild-type Bdellovibrio is seen to deform and
‘squeeze’ through an entry pore thinner than the predator cell
Structure of the Bd3460 self-protection ankyrin repeat protein.
The structure of the exported, periplasmic region of Bd3460
(amino acids 26–220, hereafter referred to simply as Bd3460) was
determined from X-ray diffraction data extending to 1.85 Å
resolution (data collection and reﬁnement statistics are provided
in Supplementary Table 1). The structure is comprised of six
sequential ankyrin repeats (AR1–AR6), which stack together to
form the conventional ‘cupped hand’ fold representative of ARPs,
with the short b-strand ‘ﬁngers’ projecting out from the concave
‘palm’ (Fig. 4a). The repeat regions largely conform to the 33
amino acid length of regular ARP motifs, with the longest loop
present between AR3 and AR4 (Fig. 4a, sequence representation
in Supplementary Fig. 7). The region surrounding the AR3:AR4
loop at the ‘centre’ of Bd3460 displays three major deviations
from the ankyrin structural consensus. Firstly amino acids
V126 to G131 form an extended loop that differs from the usual
tight turn present between the ﬁngers of the other repeats of
Bd3460/standard ARPs. Secondly, the crossover region at the end
of AR4 (K154 to N158) is a-helical in nature much like that
observed in the ARP IkBa(ref. 17). Thirdly, the repeats of
Bd3460 can be grouped such that AR1:4 and AR5:6 stack with a
regular angular periodicity, but AR5 is twisted with respect to
AR4. This 4 þ2 arrangement of repeats results in a partial cleft
between these two subdomains, lined by D132, M136, A139,
Q140, A167, A170 and V171. The cumulative effect of the three
deviations from consensus structure is that the central AR3:AR4
loop projects further from the core of Bd3460 than the other
loops, and at a relatively more acute angle. Bd3460 displays
conformational sampling such that chains A to E adopt different
relative ﬂexation between AR4 and AR5 (Fig. 4b).
Architecture of Bd3460 in complex with multiple targets.We
next utilized a modiﬁed version of our original Bd3459 construct
(starting post signal peptide with K38 mutated to become the new
N-terminal methionine) that represents a more ‘native’ signal
peptide-processed form of the DD-endopeptidase6. This version
(hereafter simply referred to as Bd3459), was co-expressed with
the exported domain of Bd3460 and the structure of this complex
determined to 1.36 Å resolution (Fig. 5a). The Bd3459:Bd3460
interaction reveals that AR1-3 of the self-protection protein are
located over the endopeptidase active site cleft, whereas AR4-6
contact the ﬁnal a-helix of the transpeptidase domain
(a9, Fig. 5b). This orientation of binding situates the ankyrin
‘cupped hand’ loops toward the rear face of the enzyme, such that
the active site is blocked by the helix-turn-helix section of the
AR repeats—this inhibition mode is B180°to that commonly
observed for AR-mediated protein interactions, but has precedent
in some ARP complexes e.g., p16Ink4a:Cdk6 (ref. 18).
The Bd3459:Bd3460 interface buries 2372 Å2of surface area,
and is largely polar in nature; 13 hydrogen-bonds, 1 salt bridge,
125 non-bonded contacts; indicating complexation largely via
shape complementarity. Upon comparison with our structures of
the uncomplexed proteins, Bd3459 does not alter in conformation
upon binding, whereas Bd3460 undergoes further ﬂexation
around the region between AR4-AR5 (Fig. 4b). This observation
explains the 4 þ2 arrangement of the repeats, such that the gap
between AR4 and AR5 allows Bd3460 to undergo an induced
ﬁt and contact a patch of Bd3459 around the 346-351 loop
and C-terminal end of helix a9. This interaction would not be
possible if Bd3460 retained the extended conformation of the
T=30T=0 T=180T=60 T=240
Figure 1 | Periplasmic localization of Bd3460 protein. Epiﬂuorescence
phase contrast microscopy of Bdellovibrio with a Bd3460::mCherry tag.
Fluorescence is seen in the small, attack phase cells at times 0 and
240 min, and increases as the Bdellovibrio enter the prey, which rounds up
to form a ‘bdelloplast’. As the Bdellovibrio cell grows inside the bdelloplast,
the ﬂuorescence becomes dissipated in the larger, cylindrical cell
(T¼180 min). Scale bar, 1 mm.
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uncomplexed state. To the best of our knowledge, this
signiﬁcant conformational rearrangement following ARP target
complexation is unique.
The use by B. bacteriovorus (and related periplasmic predators)
of multiple DD-endopeptidases to decrosslink prey wall, and
our observation of speciﬁc neutralization of Bd3459 by Bd3460
raised the question as to whether a similar mechanism is used to
protect against Bd0816. Bd0816 expression was toxic but was
circumvented by mutating the active site Serine residue to
Alanine (S58A). The resulting 2.48 Å structure of the
Bd0816:Bd3460 complex reveals a conserved mode of binding
between the ARP self-protection protein and both predatory
DD-endopeptidase targets (Fig. 6a,b).
The Bd0816:Bd3460 complex could be superimposed onto the
Bd3459:Bd3460 co-ordinates with an RMSD for equivalent atoms
of 0.76–0.94 Å (using different heterodimers of Bd0816:Bd3460
from the asymmetric unit), the conformation of Bd3460 being in
agreement with the induced-ﬁt observation outlined above.
Bd0816 is largely structurally equivalent to Bd3459, with a few
small differences in surface-exposed loops (Fig. 6b; loops involved
in Bd0816 oligomerization). It is striking that we observe a
trimeric form of Bd0816 (burying 1,041 A2of surface area per
monomer, on the borderline for statistically signiﬁcant
oligomers19). In-vitro characterization of the Bd0816:Bd3460
complex suggests the 1:1 heterodimer likely represents the
dominant form in solution (Supplementary Fig. 8). Comparison
of the residues involved in both complexes illustrates that the
endopeptidase:self-protection protein interface is conserved
(Fig. 6c), and is likely to be representative of protection
mechanisms in related predators. The B. bacteriovorus
housekeeping self endopeptidase Bd3244 (required for growth
in walled bacteria) has notable sequence differences to the
predation endopeptidases6, several of these map onto the Bd3460
interface unique to the predatory enzymes, indicating that
*** ** ** **
Attachment time (min)
Entry time (min)
E. coli (pBd3460)
E. coli (pBd3460)
E. coli (pBd3460)
E. coli (pBd1180)
Bdellovibrio strain: Bdellovibrio strain:
HD100 ΔBd3459 ΔBd0816
ΔBd3459 ΔBd3459ΔBd0816 ΔBd0816
Figure 2 | Heterologous Bd3460 protects prey from rounding and affects predator entry. (a) Graphs showing the average roundness coefﬁcient of
bdelloplasts from phase contrast images. Roundness analysis was carried out on wild-type and endopeptidase knockout-mutant Bdellovibrio infected E. coli
prey cells heterologously expressing Bd3460. Images were taken 90min post-invasion and the roundness of infected prey cells were analysed using ImageJ
software. Roundness of bdelloplasts is reduced in all cases by IPTG induction of bd3460. A negative control of induction of bd1180, a different ankyrin repeat
protein, did not reduce roundness, giving values similar to wild type (0.85 c.f. 0.90 published in Lerner et al.6) Error bars show 95% conﬁdence intervals
and statistical analysis of the means were compared with WT (*Po0.05; ***Po0.001 as determined by Student’s t-test). Data are taken from at least
two independent experiments (n460). (b) Histograms of mean times for attachment (lefthand panel) and invasion (righthand panel) by B. bacteriovorus
HD100 wild type (straight line ﬁll), DBd0816 (diagonal line ﬁll) and DBd3459 (solid ﬁll) strains infecting E. coli S17-1 (pBd3460). Mean attachment time
was measured from initial Bdellovibrio contact with the outside of prey cell to the start of traversal through the prey cell wall. Mean invasion time was
measured from the start of traversal through the prey cell wall to not being visible outside the prey cell, that is, being completely within the prey cell. At
least two independent experiments were carried out (n450) with error bars showing 95% conﬁdence intervals and statistical analyses shown (**Po0.01
***Po0.001 in Student’s t-test).
ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9884
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self-wall maintenance would not be compromised by off-target
complexation by Bd3460. The action of Bd3460 to neutralize two
differing targets suggests intricate co-evolution, analysis of which
will be revealed by large-scale sequencing of further predatory
The DD-endopeptidase substrate peptidoglycan is a large (and
branched) molecule, and our structures indicate that the binding
interface of the endopeptidase:Bd3460 complexes blocks substrate
turnover without the need for extensive, active site-centered
contacts (for example, like those observed in the b-lactamase-
inhibitory protein:TEM b-lactamase complex20). The availability
of the active site catalytic serine of the endopeptidase in the
Bd3460-bound form (Fig. 5c) agrees well with the ﬁnding that
acylation of Bd3459 with penicillin G had only a minor effect on
complex formation. Indeed, we were able to demonstrate this
further by acylating pre-grown Bd3459:Bd3460 complex crystals
with penicillin G (Supplementary Fig. 9), hence Bd3459 retains
activity and acylation propensity in complex and endopeptidase
function is blocked via steric occlusion with Bd3460.
Model for self-protection during prey invasion by predators.
The in vivo and in vitro evidence suggest a model where Bd3460
is exported to the periplasm and persists there, acting to inhibit
Bd3459 and Bd0816 function after folding in the periplasm and
before reaching the cell wall target in prey. The protein complexes
show that the interaction face involves the signal peptide cleavage
site for Bd3459/Bd0816, hence binding may potentially be
strongest to the mature form of these enzymes and thus not
interfere with secretion and/or processing by signal peptidase,
with Bd3460 forming protective complexes only in the periplasm.
The simplest scenario for self-protection, coupled to effective
rounding of prey, would be to retain Bd3460 and differentially
secrete Bd3459/Bd0816. The induced ﬁt of Bd3460 upon binding
the DD-endopeptidases could potentially be exploited to lessen
any interaction and aid Bd3459/Bd0816 ‘stripping’ during ﬁnal
export into prey. Periplasmically retained Bd3460 (visualized as
an abundant Bd3460:mCherry ﬂuorescent signal) would be able
to inhibit Bd0816, compensating for its expression from its
genetic locus outside of the bd3459/bd3460 operon.
Heterologous expression of Bd3460 in prey did not abolish
predator entry (as for the double endopeptidase mutant
Bdellovibrio) although deletion of Bd3460 in Bdellovibrio
produced a cell that puffed up and did not enter prey.
Furthermore it is clear that prey naturally acquiring the gene to
express Bd3460 in their periplasm would not be immune
from Bdellovibrio entry, consistent with the observations that
Bdellovibrio have a wide prey range and that natural resistance
is not seemingly easily acquired4. The ‘pufﬁng up’ of the
DBd3460 Bdellovibrio after a period of binding to and
recognizing the prey cell may represent a useful tool to discern
The acquisition/source of the bd3460 gene during the evolution
of invasive predatory Bdellovibrio is as yet unknown. The ankyrin
repeat residue conservation complicates homology searches, but
the highest-ranked BLAST hit for Bd3460 from a non-predatory
bacterium is an ARP from the spirochete Leptospira kirschneri
(UniProt accession code K6IH47; in an operon with a protease).
Ancient lateral gene transfer to the Bdellovibrio genome of genes
from spirochaete genomes has been noted by Gophna et al.21 and
is predicted to represent key stages in the evolution of predation.
Figure 3 | DBd3460 Bdellovibrio self-round upon initiating prey cell
entry. Epiﬂuorescence phase contrast microscopy of Bdellovibrio (small,
phase dark, comma-shaped cells) preying upon E. coli prey cells which have
periplasms constitutively ﬂuorescently labelled by a pMal::mCherry fusion.
A cartoon representation is presented above each. (a) Control using host
independent strain HID22 which is wild-type for Bd3460 (Bb wt) and
shows typical attachment to and entry into the prey cell which is rounded
up in the process. (b)DBd3460 host independent strain (Bb D3460)
attaches to the prey cell in a manner similar to the wild-type control, but
then rounds up itself, preventing entry into the prey cell. (c) Representative
electron micrographs showing the different stages of attachment,
Bdellovibrio rounding, and prey rounding. Scale bars, 1 mm ; time is
indicated in minutes.
AR2 AR3 AR4 AR5
Figure 4 | Structure of the endopeptidase self-protection protein
Bd3460. (a) Sequential ankyrin repeats (AR) form the core of Bd3460,
with a crossover helix (a*) between AR4/5; the AR4:AR5 packing differs
from the other repeats, leading to a ‘4 þ2’ arrangement. (b) View B90°
from that in a, demonstrating relative ﬂexation between the extended
(orange, unbound chain A) and endopeptidase target-complexed (blue)
forms of Bd3460, residues Y174 and Q210 represented in stick form to
guide interpretation (AR1-4 conformation common to all forms, coloured
white; chains B–E of unbound form represent states of intermediate
conformation and are rendered transparent for clarity).
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The acquisition and diversiﬁcation of an ancient ARP may have
increased selection for the gene duplication and diversiﬁcation of
a housekeeping DD-endopeptidase (like the modern Bd3244 for
self-wall modiﬁcation and growth) and its recombination at the
ARP gene locus. Ultimate co-expression of the two may have
allowed the predatory DD-endopeptidase gene(s) to evolve from
the housekeeping form without causing damage to the predator
cell wall. The prevalence of ARPs as effectors in intracellular
parasites and symbionts such as Coxiella,Wolbachia and
Legionella is also of note10,11, and a recent report detected
homology between the mevalonate-metabolizing proteins of
Bdellovibrio and Legionella pneumophila, suggesting that gene
transfer between the two is possible22. Other ARPs can be
identiﬁed in the B. bacteriovorus HD100 genome, one of
which (Bd1180) is in an operon with the peptidoglycan
LD-transpeptidase Bd1181 (ref. 23), hence our identiﬁcation of
ankyrin repeat protein Bd3460 as a key player in self-protection
may lead us to identify important enzymes in the predatory
process by locating putative immunity protein:effector pairs and
we predict that Bd1181 and Bd1180 will act in a similar paired
way to manipulate prey while protecting self.
In summary, we conclude that we have identiﬁed and
characterized the ﬁrst ever self-protection protein encoded
by predatory bacteria—ankyrin repeat protein Bd3460 from
Bdellovibrio inhibits the prey wall decrosslinking enzymes
Bd3459/Bd0816 and in doing so protects the predator from
the shape transition that this catalyses in prey. The Bd3459/
Bd0816:Bd3460 relationship is integral to Bdellovibrio
predation, regulating prey entry and self-protection (Bd3460)
and also niche formation and population ﬁtness (Bd3459/
Bd0816). We therefore regard the Bd3459/Bd0816:Bd3460
interaction as a key predatory adaptation and a signiﬁcant step
in understanding the hierarchical biochemical timeline of staged
prey recognition and invasion and the evolution of an
RNA isolation from predatory cycle and RT-PCR analysis.Synchronous
predatory infections of B. bacteriovorus HD100 by predation with MOI42in
100 ml 2 mMCaCl
/25mMHEPES buffer pH 7.6 on E. coli S17-1 as well as S17-1
alone were set up as previously described24. Samples were taken throughout the
timecourse and total RNA isolated from them. RNA was isolated from the samples
using a Promega SV total RNA isolation kit with the RNA quality being veriﬁed by
an Agilent Bioanalyser using the RNA Nano kit. RT-PCR was performed with the
Qiagen One-step RT-PCR kit with the following reaction conditions: One cycle
50 °C for 30 min, 95 °C for 15 min, then 25 cycles of 94 °C for 1 min, 48 °C for
1 min, 72 °C for 2 min and ﬁnally a 10 min extension at 72 °C after the 30 cycles,
and ﬁnally a 4 °C hold. All experiments were carried out with at least two biological
repeats. Primers used to anneal to bd3460 were 50-TTTCCTCGCGGGCCTTC
TGC-30and 50-GGCCAGATCACCTTGTTCCGCC-30. Primers used to anneal to
bd3459 were 50-ACAAGTCCCGCTCTGACTGGG-30and 50-GTACTTGATTGC
Fluorescent tagging of Bd3460.The bd3460 gene was cloned into the
pK18mobsacB mobilizable vector in such a way as to fuse the gene at the
C-terminus with the mCherry gene, using the NEB Gibson assembly kit. The
primers used to amplify bd3460 were: 50-CGACGGCCAGTGCCAATGAAAAAAT
and to amplify mcherry: 50-CAAAAAGAAAATGGTGAGCAAGGGCGAG-30
and 50-CTATGACCATGATTACGTTACTTGTACAGCTCGTCCATG-30. This
construct was introduced to Bdellovibrio via conjugation from E. coli S17-1 donor
strain, mating overnight at 29°C with B. bacteriovorus HD100 on a nitrocellulose
ﬁlter on a PY (10 g l 1peptone, 3 g l 1yeast extract) agar plate, before selection
for exconjugants by 50 mgml1kanamycin sulphate in YPSC double layer agar
plates (1 g l 1peptone, 1 g l 1yeast extract, 0.5 g l1anhydrous sodium acetate,
0.25 g l 1M
O, pH 6.8), as described previously25,26.
Heterologous expression of Bd3460 and roundness measurement.Phase
contrast time-lapse microscopy was carried out on predation by Bdellovibrio of
E. coli S17-1 harbouring the pET26b expression vector with the bd3460 gene under
the control of an IPTG inducible promoter. The prey E. coli were grown in YT
broth (8 g l 1bacto-tryptone, 5 g l 1yeast extract, 5 g l 1NaCl, pH 7.5) for 16 h
with shaking at 200 r.p.m. with kanamycin sulphate selection at 50 mgml1either
with or without 200 mgml1IPTG induction before being washed and con-
centrated ﬁve times in Ca/HEPES buffer by centrifugation for 2 min at 17,000g.
Bdellovibrio cultures were grown for 16 h as a prey lysate in 50 ml Ca/HEPES buffer
on 3 ml E. coli S17-1 prey as described previously22,24 before being concentrated
A207 S208 N209
Figure 5 | Details of the Bd3459 endopeptidase:Bd3460 auto-immunity protein complex. (a) An extensive interaction places all six ankyrin repeats
of Bd3460 (ribbon form, red) over the upper, transpeptidase lobe of Bd3459 (ribbon form, helices sky blue, strands yellow; active site serine in stick form
and denoted by asterisk; active site extended loop, dark blue). A small pocket of solvent exists at the protein interface. (b) Orthogonal view from a,
demonstrating that AR1:6 of Bd3460 effectively wrap around the ﬁnal helix of the Bd3459 transpeptidase domain, interacting via the helix-turn-helix
section of the repeats. (c) Interacting partners have been rotated like an open book from orientation in a, Bd3459 90°to left, Bd3460 90°to right.
The interaction face of Bd3459 (blue) is comprised of two continuous regions that abut, but do not comprise the active site cleft (catalytic serine coloured
red). In contrast, the interacting face of Bd3460 (pink) is formed from a single face of the protein.
ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9884
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50 times in Ca/HEPES buffer by centrifugation for 2 min at 17,000g. The
concentrated preparations of predator and prey were mixed and immediately
added to a microscope slide with a layer of 0.3% agarose in Ca/HEPES buffer to
immobilise the prey cells. Immobilized cells were visualized using a Nikon Eclipse
E600 microscope using a 100 objective lens (numerical aperture (NA), 1.25) and
an exposure time of 0.1 s. Images were acquired using a Hamamatsu Orca ER
camera and the Simple PCI software (version 6.2 from Digital Pixel). An H101A xy
motorized stage (Prior Scientiﬁc) allowed precise revisiting of different locations on
the slide (minimum step size, 0.01 mm), and a frictional z-axis controller (minimum
step size, 2 nm) in conjunction with the Simple PCI software allowed ﬁne
autofocusing on immobilized developing bdelloplasts. Images were enhanced using
either (or both) the ‘sharpen’ and ‘smooth’ tools in the Image J software to provide
additional clarity. To investigate the differing bdelloplast shapes quantitatively,
traces of the bdelloplasts in 90 min images were made and measures of ellipticity
were taken using the Image J software to ﬁnd an average ‘roundness’ coefﬁcient for
each invading Bdellovibrio strain and prey combination.
Co-expression of Bd3459 and Bd3460 in E. coli.The bd3460 gene was intro-
duced into the pET26b vector by recombineering, using the primers 50-CCTCGC
CTTTTGC-30. An apramycin resistance cassette was then introduced in place of
the kanamycin resistance cassette. The Bd3459 construct in the pBADHisA vector,
with Bd3459 under control of a promoter inducible by arabinose, has been described
previously6, and was modiﬁed to introduce an apramycin resistance cassette in place
of the ampicillin or kanamycin resistance cassette. The two vectors could then be
maintained in E. coli with apramycin and kanamycin selection. E. coli Top10
(Bd3459pBADapra þBd3460pET26bkan) were backdiluted to OD
of 1.0, pre-
incubated 1 h with selection (with or without IPTG), then 10ul was put on pads
consisting of 1% agarose YT þ0.2% arabinose on slides for microscopy with images
acquired every 150 s with the microscopy setup as above. Images at every hour were
then analysed by manually scoring cells as intact or damaged and numbers were
expressed as a percentage. As a result of cell growth, it was not possible to accurately
score images after 4 h as large damaged cells merged together. A minimum of two
biological repeats and N¼220–1,062 for each timepoint, with more cells counted at
the later timepoints. T-test gave values of Po0.001 for t¼2, 3 and 4 h.
Cloning of Bd3460 and co-expressed endopeptidases.Overexpression con-
structs were generated by a restriction-free cloning strategy27. In brief, nucleotide
primer pairs complementary to both the target gene (at the 30end of each primer)
and destination vector (at the 50end of each primer) were used to generate PCR
products which were subsequently inserted into plasmids by a second PCR
Primer pairs 50-GTTTAACTTTAAGAAGGAGATATACATATGTCAGGGA
TTCTTTTTGGAGAGAGCTTTTGC-30were used to amplify the region encoding
the predicted secreted form of Bd3460 (starting at Ser26 with mutation of Ala25 to
become the new N-terminal methionine, and placing a non-cleavable LEH
tag on the C-terminal end of the protein) for cloning into a modiﬁed version of the
expression plasmid pET41 (Novagen, altered to remove glutathione S-transferase
A new variant of the predicted secreted form of Bd3459 was also cloned into
modiﬁed pET41 using primers 50-TTTAACTTTAAGAAGGAGATATACATA
TGGTGGTGGTGCTCG AGTTTCTTCTCTGTCGTGATAGTGTTC-30, yielding
a construct similar to that described previously but starting with codon K38M
as opposed to A37M6. Bd0816 was cloned into modiﬁed pET41 using primers
TGGAAAGATTCACAAC-30, starting at K26M.
Figure 6 | Complexation of the Bd3460 self-protection protein with the second endopeptidase partner Bd0816. (a) Heterohexameric Bd0816
complex, with a single pair (Bd0816, orange; Bd3460, red) in bold and remainder of hexamer transparent (Bd0816, yellow; Bd3460, pink).
(b) Superimposition (using Bd3460, transparent) of the related Bd3459 and Bd0816 endopeptidases (blue and orange, respectively). The largest structural
difference between the two targets forms part of the Bd0816 trimer interface (circled)—generally the folds show high equivalence. (c) Bd0816/Bd3459:
Bd3460 interaction face comparison; Bd3459 (blue) and Bd0816 (orange) display a common, conserved interface (labels in bold type, standard stick form;
located largely at the ﬁnal transpeptidase domain ahelix highlighted in Fig. 5b) at the core of the interaction, surrounded by a less conserved ‘halo’ of
variant interacting residues (labels in normal type, transparent stick form).
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For co-expression of proteins, Bd3460 was cloned into pCDF-Duet1 (Novagen)
using primers 50-GTTAAGTATAAGAAGGAGATATACATATGTCAGGGAAG
TTTGGAGAGAGCTTTTGC-30. The resultant plasmid, which contained Bd3460
sequences as described above (but not fused to a puriﬁcation tag) was used as the
destination vector for sequential cloning of Bd3459 (50-GTTTAACTTTAAGAAG
GTGGTGCTC-30) or Bd0816 (primers 50GTTTAACTTTAAGAAGGAGATA
TACCAT GGTTTATGTCAATTCCGTCTG-30and 50-CGATTACTTTCTGTTC
and Bd0816 fragments for this second cloning stage were ampliﬁed from the
corresponding pET41 derived plasmids to provide C-terminally H
The Bd3459 S70A and Bd0816 S58A mutants were generated via standard
Quikchange protocol (Stratagene). All constructs were conﬁrmed by sequencing,
and introduced into the E. coli expression strain T7 express (New England
Protein expression and puriﬁcation.For puriﬁcation of Bd3460, cells were grown
at 37 °C until reaching an OD
of B0.6, then gene expression induced with 1 mM
IPTG for 20 h at 20 °C. Harvested cells (B12 g from 1 l cell culture in TB
medium) were resuspended by tumbling in 45 ml resuspension buffer (20 mM
Hepes pH 7.2, 0.25M NaCl, 5% w/v glycerol, 20 mM imidazole and 10 mM sodium
cholate) and lysed using sonication. Unbroken cells were pelleted by centrifugation
at 6,000gfor 20 min, the supernatant clariﬁed by a second centrifugation at
200,000gfor 1 h and the ﬁnal supernatent applied to a 1 ml Hi-Trap His column,
pre-equilibrated in modiﬁed buffer A (lacking sodium cholate). Fractions were
eluted in a stepwise manner, using buffer A containing 40 and 300 mM imidaz ole.
Approximately pure fractions of Bd3460 were dialysed overnight in buffer B
(10 mM Hepes pH 7.2, 0.25 M NaCl) and concentrated to a protein concentration
of B20 mg ml 1. Bd3459 (original construct) and Bd3459 new variant (K38M
start, S70A) were both expressed and puriﬁed as reported previously for Bd3459
Similar strategies were employed for the overexpression and puriﬁcation of the
Bd3459/Bd3460 and Bd0816 S58A/Bd 3460 complexes. Buffer C (20 mM imidazole
pH 8.0, 0.4 M NaCl, 0.05% w/v Tween20) was used for resuspensio n of cells and in
the place of buffer A for the puriﬁcation of complexes. Puriﬁed complexes were
dialysed overnight into buffer D (20 mM Bis-Tris pH 6.5, 0.2 M NaCl) and were
concentrated to B25 and B30 mg ml 1for the Bd3459/Bd3460 and Bd0816
S58A/Bd3460 complexes, respectively.
Analytical gel ﬁltration experiments were performed on a HiLoad 26/60
Superdex 200 column (GE Healthcare) using buffer D (20 mM Bis-Tris pH 6.5,
0.5 M NaCl).
Crystallization and structure determination.Crystals were grown by the
hanging drop method at 18 °C, using 1 ml of protein solution mixed with an equal
volume of reservoir solution. Initial apo-Bd3460 crystallization conditions were
identiﬁed in Midas screen II condition #27 (40% v/v glycerol ethoxylate28).
Crystals of Bd3459 S70A were grown in JCSG-plus screen II condition #33
(0.1 M potassium thiocyanate; 30% w/v PEG 2000 MME). The Bd3459/Bd3460 and
Bd0816 S58A/Bd3460 complexes crystallized in JCSG-plus screen II conditions #14
(0.1 M citrate, pH 5.0; 3.2 M ammonium sulphate) and #47 (0.1M Hepes, pH 7.5;
0.2 M MgCl
; 25% w/v PEG 3350), respectively. Crystals of the Bd3459M/Bd3460
complex were incubated with reservoir solution supplemented with 2 mM
penicillin G for one hour to yield an additional, acylated complex structure.
All crystals were directly ﬂash cooled in liquid nitrogen and diffraction data
were collected at the Diamond Light Source, Oxford. Data were processed using
XDS29 and SCALA, and data ﬁle manipulations performed using the CCP4 suite of
programs30. A heavy atom derivative was obtained by growing Bd3460 crystals
directly in the presence of 300 mM Potassium Iodide (data collected on a home
, Rigaku Micromax generator). Phasing of the derivative was
accomplished using a combination of SHARP31 and PHENIX32 (FOM of 0.43,
20 I sites); the resultant phases were improved by applying manually derived
non-crystallographic symmetry operators (ﬁve independent chains are present in
the unit cell). After autobuilding in PHENIX, the remaining parts of the molecule
were built manually using COOT33 and model reﬁnement used PHENIX32
and the PDB-REDO server34. Complex structures were phased using molecular
replacement with the Bd3460 and Bd3459Misolated structures and the program
PHASER35 and built/reﬁned as outlined above. The ﬁnal models are of excellent
stereochemical quality (Table 1).
The closest non-synthetic structural neighbor of Bd3460 (as calculated by
DALI36) is the uncharacterized ARP EF0377 from Enterococcus faecalis (PDB 3hra,
RMSD 2.5 Å over 167AA alignment), although Bd3460 shares slightly higher
structural homology to various DARPins (designed ankyrin repeat proteins,
engineered for afﬁnity purposes, for example, PDB codes 4hb5, 3nog).
All structural ﬁgures were generated using the program Chimera37.
Enzyme activity measurements.Incubation of Bd3459 with isolated sacculi
(±the presence of Bd3460) and subsequent HPLC analysis of cellosyl products
(muropeptides) utilized an identical protocol to that documented in the original
Bdellovibrio endopeptidase study6.
Tryptophan ﬂuorescence ligand binding measurements.Intrinsic tryptophan
ﬂuorescence ligand binding experiments were carried out using a Hitachi F-7000
ﬂuorescence spectrophotometer. The excitation wavelength was set at 280 nm and
the ﬂuorescence emission (F
) spectra was recorded between 300–400 nm.
Puriﬁed Bd3459 was diluted with buffer B (Hepes switched to Tris) to a ﬁnal
concentration of 10 mM loaded into a quartz cuvette (ﬁnal volume of 400 ml)
equilibrated to a chamber temperature of 25 °C. Bd3460 was sequentially titrated
against Bd3459 with F
recorded between each addition. On occasions,
0.75 mM penicillin G was pre-incubated with Bd3459 before being titrated with
Bd3460. GraphPad Prism software was used to plot the change in ﬂuorescence
Table 1 | Data collection and reﬁnement statistics.
Bd3460 native Bd3460 iodine
Accession code 5CEA — 5CEB 5CEC 5CER 5CED
Space group P2
a,b,c(Å) 57.43, 99.64,
57.13, 99.18, 173.33 55.93, 65.04, 73.82 51.61, 59.17, 192.27 212.32, 237.45,
a,b,g(°) 90, 90, 90 90, 90, 90 63.89, 83.27, 83.20 90, 90, 90 90, 90, 90 90, 90, 90
Resolution (Å) 1.85 (1.95–1.85)* 2.4 (2.53–2.4) 1.93 (1.98–1.93) 1.36 (1.4–1.36) 2.48 (2.54–2.48) 2.02 (2.07–2.02)
7.0 (49.3) 6.3 (31.0) 3.6 (76.6) 3.2 (51.6) 15.6 (75.3) 6.7 (67.2)
6.0 (42.9) 1.6 (26.7) 2.5 (54.9) 2.0 (41.9) 4.6 (21.5) 3.1 (30.8)
CC 1/2w0.99 (0.65) 0.99 (0.79) 0.99 (0.78) 0.99 (0.78) 0.99 (0.85) 0.99 (0.80)
I,/sI10.0 (2.5) 34.4 (2.7) 16.2 (1.6) 23.4 (2.4) 15.1 (3.8) 16.2 (2.8)
Completeness(%) 99.0 (100.0) 89.5 (47.8) 85.7 (79.2) 97.2 (77.8) 99.0 (99.5) 99.9 (99.9)
Redundancy 3.8 (3.7) 13.9 (2.0) 3.8 (3.7) 6.0 (3.7) 13.5 (14.0) 6.5 (6.7)
Resolution (Å) 1.85 — 1.93 1.36 2.48 2.02
17.8/21.0 — 19.8/23.2 14.3/16.9 21.7/24.9 17.3/20.7
Bond lengths (Å) 0.017 — 0.016 0.011 0.014 0.014
Bond angles (°) 1.75 — 1.63 1.44 1.68 1.60
*Values in parentheses are for highest resolution shell.
wCC 1/2 is the correlation coefﬁcient between two random half data sets.
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versus [Bd3460] and data were ﬁtted to a one
site-speciﬁc binding isotherm (DF
þL), where F
the maximum change in ﬂuorescence emission, K
is the binding constant and Lis
the concentration of ligand (Bd3460).
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We are grateful to Klaus Futterer for many interesting discussions and Ana Clark for
investigative work in the initial stages of the project. This work was supported by BBSRC
grant BB/J015229/1 awarded to R.E.S. and A.L.L., and the Wellcome Trust Senior
Investigator Award (101824/Z/13/Z) to W.V. We thank beamline staff at Diamond light
source, Didcot UK.
C.L. performed experiments for heterologous expression studies in E. coli, heterologous
expression abrogating effects on predation, cloning and microscopy for ﬂuorescence
tagging, generated mutants and microscopy of mutant phenotypes and RT-PCR repeats.
A.L. and I.C. cloned constructs, expressed, puriﬁed and crystallized proteins, collected
data and determined/reﬁned/interpreted structures. R.T. screened for and conﬁrmed
mutants and performed ﬂuorescent microscopy. T.L. performed initial RT-PCR. K.B.
analysed muropeptide turnover; W.S.H. and L.J.A. performed ﬂuorescence experiments
quantifying protein interactions; D.J.L. cloned constructs; A.L.L. and R.E.S. designed the
study and wrote the manuscript with C.L., W.V. and I.C.
Accession codes: Crystallographic data have been deposited in the RCSB Protein Data
Bank under accession codes 5CEA (Bd3460), 5CEB (Bd3459 K38M new construct),
5CEC (Bd3459:Bd3460 complex), 5CED (Bd3459:Bd3460 complex acylated with peni-
cillin G) and 5CER (Bd0816:Bd3460 complex).
Supplementary Information accompanies this paper at http://www.nature.com/
Competing ﬁnancial interests: The authors declare no competing ﬁnancial interests.
Reprints and permission information is available online at http://npg.nature.com/
How to cite this article: Lambert, C. et al. Ankyrin-mediated self-protection during cell
invasion by the bacterial predator Bdellovibrio bacteriovorus.Nat. Commun. 6:8884
doi: 10.1038/ncomms9884 (2015).
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