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Journal of Bacteriology, November 2007, p. 8053-8058, Vol. 189, No. 22
0021-9193/07/$08.00+0 doi:10.1128/JB.00908-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
Iteron-Binding ORF157 and FtsZ-Like ORF156 Proteins Encoded by pBtoxis Play a Role in Its Replication in Bacillus thuringiensis subsp. israelensis
Mujin Tang,1
Dennis K. Bideshi,1,2
Hyun-Woo Park,3 and
Brian A. Federici1,4*
Department of Entomology, University of California, Riverside, Riverside, California 92521,1
Department of Natural and Mathematical Sciences, California Baptist University, 8432 Magnolia Avenue, Riverside, California 92504,2
John A. Mulrennan, Sr., Public Health Entomology Research and Education Center, Florida A & M University, Panama City, Florida 32405,3
Interdepartmental Graduate Programs in Genetics and Cell, Molecular & Developmental Biology, University of California Riverside, Riverside, California 925214
Received 9 June 2007/
Accepted 4 September 2007

ABSTRACT
We recently identified a minireplicon of pBtoxis from
Bacillus thuringiensis subsp.
israelensis that contained an operon encoding
two novel proteins (ORF156 and ORF157), both of which are required
for replication. ORF157 contains a helix-turn-helix motif and
shares no homology with known plasmid replication proteins (Rep),
and ORF156 contains the signature motif present in FtsZ/tubulin
proteins, the latter of which are known to function in cell
division and chromosome segregation. Here we show that the minimal
sequence composed of four 12-bp imperfect direct repeats (iterons)
in the pBtoxis minireplicon was sufficient to replicate a reporter
plasmid in
B. thuringiensis subsp.
israelensis when ORF156 and
ORF157 functions were provided in
trans. To further investigate
the roles of ORF156 and ORF157 in pBtoxis replication, six-histidine-tagged
recombinant rORF156 and rORF157 proteins were purified from
Escherichia coli and used in electrophoretic mobility shift
assays. Our results demonstrated that rORF157, but not rORF156,
binds specifically to the pBtoxis iterons, suggesting that ORF157
functions as a Rep protein. Although rORF156 did not bind to
the iteron sequence, we showed that it bound to rORF157-DNA
complexes. In addition, we showed that rORF156 has GTPase activity
characteristic of the FtsZ/tubulin superfamily of proteins.
Taken together, these results suggest that the iterons compose
the minimal replication origin (
ori) of pBtoxis and that ORF157
and ORF156 are involved in the initiation of pBtoxis replication
and possibly in the segregation and partitioning of this plasmid
to daughter cells.

INTRODUCTION
The large 128-kb plasmid, pBtoxis, in
Bacillus thuringiensis subsp.
israelensis encodes all major endotoxin proteins (Cyt1Aa,
Cry4A, Cry4B, and Cry11A) responsible for the mosquito larvicidal
activity of this strain (
3,
7,
17). The molecular mechanism
by which pBtoxis replicates has not been established, though
preliminary evidence indicates it has unique features (
18).
For example, we recently identified a minireplicon of pBtoxis
that contains an operon with two open reading frames (ORF),
pBt156 and pBt157, coding for two novel proteins, respectively,
ORF156 (54.4 kDa) and ORF157 (11.8 kDa) (
18). The ORF157 protein
contains a helix-turn-helix motif common in a wide variety of
protein families, including those involved in transcription
and DNA replication (
1), whereas ORF156 contains a sequence
motif present in the FtsZ/tubulin superfamily (
3,
18) and ORF45
(RepX) encoded by the virulence plasmid, pXO1, in
Bacillus anthracis (
19). An apparent homologue of ORF157 is absent in pXO1. Despite
the presence of conserved domains in ORF157, ORF156, and RepX,
these proteins share no homology with proteins known to function
in plasmid replication and partitioning (
1,
19). Nevertheless,
Tang et al. have shown that ORF156 and ORF157 are required for
minireplicon replication (
18). Indeed, Tinsley and Khan (
19)
have reported the RepX is also essential for replicating a pXO1-derived
minireplicon and have proposed that the FtsZ-like proteins encoded
by large plasmids in members of the
Bacillus cereus sensu lato
group (
B. thuringiensis,
B. anthracis, and
Bacillus cereus)
represent a novel family of initiator proteins involved in replicating
large virulence plasmids. Though the specific functions of ORF156
and ORF157 in pBtoxis replication are unknown, in a more recent
study Larsen et al. (
12) showed that ORF156 fused to the green
fluorescent protein (TubZ-GFP) assembles directional linear
polymers characteristic of the tubulin superfamily of proteins
and have also provided evidence that ORF157 (TubR) has a negative
effect on ORF156 levels.
The pBtoxis minireplicon also contains two putative cis elements; a putative dnaA box motif (TTTTCCACT) similar to those found in plasmids in Escherichia coli and Bacillus subtilis, to which initiator DnaA proteins bind; and iterons known to be essential for initiating replication of large theta-replicons (6, 10, 11). Iterons function as binding sites for plasmid-encoded Rep proteins and in the formation of higher-order structures of iteron-initiator complexes that are required to initiate plasmid replication (4, 14, 15). Similar to other large plasmids with A+T-rich iterons, the pBtoxis iterons are composed of four 12-bp A+T-rich direct imperfect repeated sequences (T[A/T][A/T][C/A][G/A]GTTTA[A/C][A/C]), which together with the putative dnaA box are found upstream of the pBt157 gene (18).
To date, little is known about the molecular basis for DNA replication of the large virulence plasmids of the B. cereus sensu lato group. The novel features of the plasmid-encoded FtsZ tubulin-like proteins, ORF156 and RepX, and the helix-turn-helix-containing ORF157 suggest a conserved but unknown mechanism for propagating and restricting these plasmids within a narrow host range. Here, we demonstrate that the 48-bp iterons alone were sufficient to support replication of a reporter plasmid propagated in B. thuringiensis subsp. israelensis in which ORF156 and ORF157 functions were provided in trans by parental pBtoxis, demonstrating that the iterons compose the minimal replication origin (ori) of the pBtoxis minireplicon. Furthermore, we used electrophoretic mobility shift assays (EMSAs) to show that ORF157, but not ORF156, binds with high specificity to the iteron sequence, suggesting that this binding event initiates pBtoxis replication. Although ORF156 is not an iteron-binding protein, we show that it is an Mg2+-dependent GTPase that interacts directly with ORF157-DNA complexes, thereby implicating its role as a replication initiator protein.

MATERIALS AND METHODS
Bacterial strains, DNA manipulation, and transformation.
The bacterial strains described here are listed in Table
1.
Luria-Bertani medium was used to culture
Escherichia coli,
B. thuringiensis subsp.
israelensis 4Q7, and
B. thuringiensis subsp.
israelensis 4Q5. Antibiotic concentrations for bacterial selection
were as follows: 100 µg/ml ampicillin and 10 µg/ml
chloramphenicol. DNAs from
B. thuringiensis and
E. coli were
extracted using the plasmid Midi and Maxi kits (QIAGEN) and
the Wizard plus minipreps DNA purification system (Promega).
DNA fragments were isolated from agarose gels using the QIAquick
gel extraction kit (QIAGEN) and ligated using the Fast-Link
DNA ligation kit (Epicenter). PCR was performed with the Expand
Long Template PCR system (Roche Molecular Biochemicals) in a
Px2 system thermocycler (Thermo Hybaid) for 30 cycles as follows:
94°C for 30 s, 55°C for 30 s, and 68°C for 2 min.
Transformation of
B. thuringiensis subsp.
israelensis 4Q7 and
B. thuringiensis subsp.
israelensis 4Q5 with 5 µg plasmid
DNA was performed as described previously (
21,
22).
Construction of recombinant plasmids.
The plasmids described here are listed in Table
1. To construct
pUCCl, a vector that does not replicate in
B. thuringiensis,
the 1.0-kb Sau3AI/HpaII fragment containing the chloramphenicol
resistance gene from pC194 (
9) was cloned into the blunted NdeI
site of pUC19. Plasmid pUCSw, which contained the minireplicon
of pBtoxis (
18), was constructed by cloning the 2.2-kb SwaI
fragment from pBtKp (Table
1) in the SmaI site of pUCCl. Plasmid
pUCP (Fig.
1), which contained the 191-bp sequence upstream
from pBt157 was constructed by inserting a PCR fragment amplified
with primers pP-F and pP-R (Table
2) into the HindIII and PstI
sites in pUCCl. Plasmid pUCID (Fig.
1), which contained the
four 12-bp-iteron sequence and the 37-bp spacer followed by
the putative
dnaA box motif (5'-TTTTCCACT-3'), was constructed
by inserting a 97-bp PCR fragment amplified with primers pIDna-F
and pIDna-R (Table
2) into the HindIII and PstI sites in pUCCl.
Plasmid pUCIDM, which was identical to pUCID except, for having
the putative
dnaA box motif replaced with 5'-CCCCAAGAC-3', was
constructed using plasmid pUCID as the template and primers
pIDM-F and pIDM-R; the ScaI/PstI-digested 1.8-kb amplicon was
ligated to the larger ScaI/PstI fragment of pUCCl to generate
pUCIDM. Plasmid pUCIS, which contained the iteron sequence and
the 37-bp spacer sequence, but lacked the putative
dnaA box
motif, was constructed by ligating the ScaI/PstI-digested 1.8-kb
fragment amplified with primers pIDM-F and pIS-R, using pUCID
as the template, with the larger ScaI/PstI fragment of pUCCl.
Plasmid pUCSD, which contained the 37-bp spacer sequence and
dnaA box motif, but not the iterons, was constructed by ligating
the NcoI/HindIII-digested 1.0-kb PCR fragment, which was amplified
with primers pSD-F and pSD-R and using plasmid pUCID as the
template, with the larger NcoI/HindIII fragment of pUCCl. To
construct pUCI (Fig.
1), a synthetic double-stranded oligonucleotide
prepared by annealing oligonucleotides 5'-CCC
AAGCTTTAAAGGTTTAAATAACAGTTTAAATTTAAGTTTAACTTTCAGTTTACACTGCAGTT-3'
and 5'-AA
CTGCAGTGTAAACTGAAAGTTAAACTTAAATTTAAACTGTTATTTAAACCTTTAAAGCTTGGG-3',
which contained the 48-bp direct-repeat iteron sequence, was
digested with HindIII and PstI (sites are underlined in sequences
above) and inserted into the same sites in pUCCl. The nucleotide
integrity of each construct was confirmed by DNA sequencing
and restriction enzyme analyses.
Expression and purification of recombinant ORF156 and ORF157 proteins.
The
L-arabinose-based pBAD/myc-his expression system (Invitrogen)
was used for synthesis of recombinant six-histidine-tagged ORF156
and ORF157 proteins, respectively, rORF156 and rORF157. The
pBt156 and pBt157 open reading frames were amplified with primers
pBAD156-F and pBAD156-R and pBAD157-F and pBAD157-R (Table
2),
respectively, digested with NcoI and XbaI, and cloned in the
same sites in pBAD/myc-hisB for expression in
E. coli TOP10
(Invitrogen). Recombinant proteins were purified using imidazole-based
buffers and Ni-nitrilotriacetic acid resin columns, according
to the manufacturer's protocol (QIAGEN). The purified proteins
were desalted and concentrated using Centricon centrifugal filters
(Millipore). Protein concentration was assayed using the Coomassie
protein assay kit (Pierce), and Western blot analysis using
anti-His C-terminal antibody (Invitrogen) was performed to confirm
purification of rORF156 and rORF157.
EMSA.
Synthetic oligonucleotides 5'-TAAAGGTTTAAATAACAGTTTAAATTTAAGTTTAACTTTCAGTTTACA-3' and 5'-TGTAAACTGAAAGTTAAACTTAAATTTAAACTGTTATTTAAACCTTTA-3', containing the 48-bp iteron sequence, were boiled for 5 min and allowed to anneal by slowly cooling to room temperature. The annealed double-stranded DNA was purified from a 15% polyacrylamide gel and then labeled with [
-32P]ATP (Amersham) using T4 polynucleotide kinase (Promega), eluted from a Micro Bio-Spin P-30 Tris chromatograph column (Bio-Rad), and quantified by scintillation. For EMSA, reaction mixtures containing 2 µl 5x gel shift binding buffer (Promega), 30 fmol of labeled iterons (25,000 cpm), and 30 pmol of rORF157 or 360 pmol of rORF156, were incubated at room temperature for 20 min, and the DNA-protein complexes were resolved in a 5% polyacrylamide gel (Bio-Rad) by electrophoresis in 0.5x TBE (0.045 M Tris-borate, 0.001 M EDTA) buffer at 100 V for 2 h. Gels were dried on Whatman paper and exposed to X-ray film.
For competition assays, binding reactions were first performed at room temperature for 10 min in binding buffer containing purified proteins and a 1,000x molar excess of either unlabeled iterons as the specific competitor or an unlabeled 30-bp DNA fragment of Herves (2), a transposable element from the mosquito, as the nonspecific competitor (Fig. 2B). After incubation, the 32P-labeled iteron was added and the reaction was continued for another 20 min at room temperature. For protein-protein interaction studies with rORF156 and rORF157-iteron complexes, both proteins were added simultaneously.
GTPase assay.
The GTPase assay was performed using the EnzChek phosphate assay
kit (Molecular Probes) with 2-amino-6-mercapto-7-methylpurine
ribose (MESG) substrate, according to manufacturer's protocol,
with and without 5 mM MgCl
2 or 10 mM MgCl
2. Reactions were initiated
by adding GTP (Invitrogen) to a final concentration of 0.5 mM.
The continuous absorbance trace at a wavelength of 360 nm reflected
P
i released from rORF156-GTP complexes followed by phosphorylase
coupling reactions with MESG. Absorption at 360 nm was measured
at 10-min intervals.

RESULTS AND DISCUSSION
Replication origin of pBtoxis minireplicon.
To identify the minimal sequences required to replicate the
pBtoxis minireplicon (
18), different fragments from the minireplicon
were cloned into the vector pUCC1 to generate the reporter plasmids
pUCSw, pUCp, pUCID, pUCIDM, pUCIS, pUCSD, and pUCI (Fig.
1).
The reporter plasmid pUCSw contained the 2.2-kb pBtoxis minireplicon
that included the pBt157 and pBt156 ORFs coding for, respectively,
ORF157 and ORF156, and the iterons and putative
dnaA box motif
(
18); pUCp contained the 191-bp sequence upstream from pBt157
with the iterons and putative
dnaA box; pUCID contained the
iterons and the 37-bp spacer followed by the putative
dnaA box;
pUCIDM contained the iterons, the 37-bp spacer, and the mutated
dnaA box; pUCIS contained the iterons and 37-bp spacer; pUCSD
contained the 37-bp spacer and putative
dnaA box; and pUCI contained
only the iterons. When these plasmids were introduced into
B. thuringiensis subsp.
israelensis 4Q7, a strain cured of native
plasmids including pBtoxis, pUCSw, but not pUCp, pUCID, pUCIDM,
pUCIS, pUCSD and pUCI, replicated under selection with chloramphenicol.
The inability of the latter six plasmids to replicate in strain
4Q7 supports our previous observation that both ORF157 and ORF156
are required for plasmid replication (
18).
When the reporter plasmids pUCSw, pUCp, and pUCID (each of which contained different fragments of the pBtoxis minireplicon but included the four 12-bp iterons and 37-bp spacer sequence followed by the putative dnaA box) were introduced into B. thuringiensis subsp. israelensis 4Q5, a strain that harbors only pBtoxis (Table 1), 110, 114, and 115 transformants, respectively, grew per 5 µg plasmid DNA under selection with chloramphenicol. When the 4Q5 strain was transformed with pUCIDM, which contained the iterons, 37-bp spacer sequence, and the mutated dnaA box motif, 110 Cmr transformants/5 µg plasmid DNA were obtained, indicating that the putative dnaA box motif was not required for minireplicon replication.
Reporter plasmids containing the iterons with (pUCIS) and without (pUCI) the 37-bp spacer sequence also replicated in the 4Q5 strains, yielding, respectively, 97 and 15 colonies per 5 µg of plasmid DNA. However, whereas transformants containing pUCIS were recovered by 24 h, those containing pUCI formed smaller colonies that appeared after 48 h of incubation. Finally, when the 4Q5 strains were electroporated with pUCSD, which contained the 37-bp spacer sequence and putative dnaA box but lacked the iterons, transformants were not recovered after repeated attempts.
In all of these experiments, the presence of pBtoxis in each recombinant strain resistant to chloramphenicol was inferred by the presence of the large crystalline inclusion composed of toxin proteins encoded by this plasmid, as observed by phase-contrast microscopy. This indicated that the autonomously replicating plasmids did not have a deleterious effect on the stability of parental pBtoxis. Importantly, to confirm that the reporter plasmids replicated in recombinant 4Q5 strains and were not propagated and selected for by recombination events with chromosomal DNA or pBtoxis, plasmids were extracted from recombinant 4Q5 strains and used to transform E. coli. These reporter plasmids replicated in E. coli under ampicillin selection. Restriction enzyme and PCR analyses showed that they were identical to those used in the autonomous replication assays in the 4Q5 strains. These results demonstrated that the iterons alone functioned as the minimal replication origin (ori) of the pBtoxis minireplicon.
ORF157 is an iteron-binding protein.
The structural organization and occurrence of the iterons, pBt157, and pBt156 in an operon and their essential role in propagating the pBtoxis minireplicon suggested that the ORF157 and ORF156 proteins interact cooperatively with the cis elements in initiating pBtoxis replication. To determine whether these proteins have strong iteron-binding specificity, six-histidine-tagged recombinant proteins, rORF157 and rORF156, synthesized in E. coli, were purified by affinity chromatography (Fig. 2A) and used in EMSAs with radiolabeled iterons or unlabeled specific (iterons) and nonspecific competitor DNA (Fig. 2B). Whether the six-histidine tags in the recombinant proteins influenced the results observed in our study is not known. Nevertheless, a marked electrophoretic mobility shift was observed when rORF157 was incubated with the substrate-specific labeled iteron probe in the absence or presence of the nonspecific competitor (Fig. 2C, lanes 1 and 3). When rORF157 was preincubated with unlabeled iterons, followed by the addition of labeled iterons, a shift in mobility was not observed due to saturation of the protein with the unlabeled specific probe (Fig. 2C, lane 2). These results demonstrate that the rORF157 binds to the pBtoxis iterons with high specificity. In similar assays, no complexes were observed with rORF156 and the labeled iterons in either the absence or presence of unlabeled specific and nonspecific competitors (Fig. 2C, lanes 4, 5, and 6). These results demonstrate that ORF156 is not an iteron-binding protein.
ORF156 binds to ORF157-iteron complexes.
To further study the putative role of ORF156 in pBtoxis replication, EMSAs were performed to determine whether this protein could interact with rORF157-iteron complexes. These assays clearly demonstrated that rORF156 bound the rORF157-iteron complexes, probably through rORF156-rORF157 protein-protein interactions, resulting in a larger electrophoretic mobility shift (Fig. 3). The extent of the shift was dependent on the relative ratios of the two proteins used in the assay. For example, when the ratio of rORF157 was kept constant (30 pmol), a one- or twofold increase in rORF156 (30 or 60 pmol) had little effect on the shift of the rORF157-iteron complexes (Fig. 3, lanes 7 and 8). In contrast, by increasing the molar ratios of rORF156 to rORF157 to 4:1, 8:1, and 12:1, corresponding increases in mobility shifts of protein-DNA complexes were observed (Fig. 3, lanes 4, 5, and 6).
Putative roles of ORF157 and ORF156 in pBtoxis replication.
Although proteins other than ORF157 (11.8 kDa) could interact
with the pBtoxis iterons, the iteron-binding specificity of
this protein suggests that its function is similar to those
of other plasmid-encoded Rep proteins, including RepE (37 kDa)
and RepA (29 kDa) (
6,
8,
16). Rep proteins are known to interact
directly with genome-encoded DnaA to form multiprotein complexes
that catalyze the initiation of plasmid replication (
4,
13).
In addition, the binding of RepA to
cis elements represses transcription
from the
repA promoter, thereby providing a mechanism for autoregulating
plasmid replication and copy number. Whether ORF157 functions
as an autoregulator of transcription or pBtoxis replication
is unknown. However, recent work by Larsen et al. (
12) showed
that in a heterologous system using
E. coli as a host, in the
absence of ORF157, recombinant ORF156-GFP levels were 4.5-fold
higher than in the presence of ORF157. Therefore, it is likely
that ORF157 functions as a negative regulator of ORF156.
The ORF156 protein contains a motif (GGGVGTG) conserved in all members of the tubulin/FtsZ superfamily (PROSITE motif PS00227: [S/A/G]GGTG[S/A/T]G) that is involved in Mg2+-dependent GTP binding and hydrolysis (3, 5, 20), an enzymatic activity demonstrated for rORF156 in the present study (Fig. 4). Tinsley and Khan (19) have demonstrated that this motif is required for RepX function. However, as GTP was not included in our EMSAs, it is unlikely that the GTPase activity is required for the recruitment and assembly of ORF156 with the ORF157-iteron complex.
While favoring a model that ORF156 binds ORF157-iteron complexes,
we cannot exclude the possibility that other proteins encoded
by pBtoxis have a similar function. However, our observation
that rORF156 physically interacts with the rORF157-iteron complexes
in vitro suggests a functional role for ORF156 based on what
is known about the function of the tubulins and FtsZ proteins.
The polymer-forming GTPases that compose the tubulin/FtsZ superfamily
are similar to eukaryotic tubulins and are essential for cell
division in prokaryotes (
20). Tubulins assemble directional
linear polymers that participate in a number of cytoskeletal
processes in eukaryotes, including DNA segregation (
12). In
contrast, FtsZ proteins assemble into a ring structure, the
so-called "Z-ring," in a GTPase-dependent manner on the inner
surface of the cytoplasmic membrane and recruit cytoplasmic
proteins that mediate progressive septum invagination and subsequent
cell division (
20). Interesting, Larsen et al. (
12) have demonstrated
the recombinant ORF156-GFP (TubZ-GFP) forms dynamic linear polymers,
suggesting that ORF156 is a novel type of tubulin-based cytoskeletal
component in bacteria. Taken together, it is tempting to suggest
that the interaction of ORF156 and the ORF157-iteron complex
facilitates the segregation and partitioning of pBtoxis in daughter
cells during cell division. Additionally, the role of ORF156
could be to mediate interactions between iteron-bound ORF157
and other proteins involved in pBtoxis replication.

ACKNOWLEDGMENTS
We thank Jeffrey J. Johnson for technical assistance during
this study and P. W. Atkinson (Department of Entomology, University
of California, Riverside) for providing the nonspecific competitor
DNA used in this study.
This research was supported by a grant to B.A.F. from the U.S. National Institutes of Health (AI 145817).

FOOTNOTES
* Corresponding author. Mailing address: Department of Entomology, University of California, Riverside, Riverside, CA 92521. Phone: (951) 827-5006. Fax: (951) 827-3086. E-mail:
brian.federici{at}ucr.edu 
Published ahead of print on 14 September 2007. 

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Journal of Bacteriology, November 2007, p. 8053-8058, Vol. 189, No. 22
0021-9193/07/$08.00+0 doi:10.1128/JB.00908-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
This article has been cited by other articles:
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Chen, Y., Erickson, H. P.
(2008). In Vitro Assembly Studies of FtsZ/Tubulin-like Proteins (TubZ) from Bacillus Plasmids: EVIDENCE FOR A CAPPING MECHANISM. J. Biol. Chem.
283: 8102-8109
[Abstract]
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