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Journal of Bacteriology, November 2001, p. 6274-6281, Vol. 183, No. 21
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.21.6274-6281.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
DNA Inversion in the Tail Fiber Gene Alters the Host Range
Specificity of Carotovoricin Er, a Phage-Tail-Like Bacteriocin of
Phytopathogenic Erwinia carotovora subsp.
carotovora Er
Hoa Anh
Nguyen,1
Toshio
Tomita,1
Morihiko
Hirota,1
Jun
Kaneko,1
Tetsuya
Hayashi,2 and
Yoshiyuki
Kamio1,*
Department of Molecular and Cell Biology,
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumi-dori Amamiya-machi, Aoba-ku, Sendai
981-8555,1 and Department of
Microbiology, Miyazaki Medical College, 5200 Kiyotake, Miyazaki
899-1692,2 Japan
Received 16 April 2001/Accepted 31 May 2001
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ABSTRACT |
Carotovoricin Er is a phage-tail-like bacteriocin produced by
Erwinia carotovora subsp. carotovora
strain Er, a causative agent for soft rot disease in plants. Here we
studied binding and killing spectra of carotovoricin Er preparations
for various strains of the bacterium (strains 645Ar, EC-2, N786, and
P7) and found that the preparations contain two types of carotovoricin Er with different host specificities; carotovoricin Era possessing a
tail fiber protein of 68 kDa killed strains 645Ar and EC-2, while
carotovoricin Erb with a tail fiber protein of 76 kDa killed strains
N786 and P7. The tail fiber proteins of 68 and 76 kDa had identical
N-terminal amino acid sequences for at least 11 residues. A search of
the carotovoricin Er region in the chromosome of strain Er indicated
the occurrence of a DNA inversion system for the tail fiber protein
consisting of (i) two 26-bp inverted repeats inside and downstream of
the tail fiber gene that flank a 790-bp fragment and (ii) a putative
DNA invertase gene with a 90-bp recombinational enhancer sequence. In
fact, when a 1,400-bp region containing the 790-bp fragment was
amplified by a PCR using the chromosomal DNA of strain Er as the
template, both the forward and the reverse nucleotide sequences of the
790-bp fragment were detected. DNA inversion of the 790-bp fragment
also occurred in Escherichia coli DH5
when two
compatible plasmids carrying either the 790-bp fragment or the
invertase gene were cotransformed into the bacterium. Furthermore,
hybrid carotovoricin CGE possessing the tail fiber protein of 68 or 76 kDa exhibited a host range specificity corresponding to that of
carotovoricin Era or Erb, respectively. Thus, a DNA inversion altered
the C-terminal part of the tail fiber protein of carotovoricin Er,
altering the host range specificity of the bacteriocin.
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INTRODUCTION |
Hamon and Peron first
described a substance(s) produced by Erwinia carotovora
subsp. carotovora, the causative agent of soft rot disease
in many plant species, that is bactericidal towards the same and
related species of bacteria (7). Because of the proteinaceous nature of this bacteriocide and its narrow bactericidal spectrum, they assumed it to be a bacteriocin and designated it carotovoricin (7). Previous reports from this laboratory
showed that E. carotovora subsp. carotovora Er
produced carotovoricin Er as well as pectin lyase when it was exposed
to nalidixic acid, mitomycin C, or bleomycin (27) and that
a phage-tail-like particle was observed in the partially purified
fraction of carotovoricin Er (16, 13). Recently, we
developed a simple and efficient procedure for purification of intact
carotovoricin Er and its major structural parts by use of sucrose
density gradient centrifugation in the presence of 10 to 20% (vol/vol)
ethanol and analyzed the highly purified carotovoricin Er for its
morphology and components (21). Electron microscopy showed
that carotovoricin Er consists of an antenna-like structure, a
sheath-and-core part, a base plate, and several tail fibers
(21). It was revealed that (i) carotovoricin Er has a
length of 184 nm (from the distal end of the sheath-and-core part to
the bottom of the base plate) and a diameter of 22 nm (at the
sheath-and-core part); (ii) the antenna-like structure at the distal
end of the sheath-and-core part is a rod structure with a length of 54 nm, which has never been reported for pyocin R (12) or
xenorhabdicin (26); (iii) the sheath is a contractile cylindrical structure surrounding an inner core, which is visible in
contracted carotovoricin Er; and (iv) the tail fibers have a length of
63 nm. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of the purified major parts of carotovoricin Er showed that
the sheath, core, and tail fiber consist of single major proteins of
50, 19, and 68 kDa, respectively (21). In addition to
these proteins, protein bands corresponding to 78, 76, 46, 44, 39, and
35 kDa were detected in the purified carotovoricin Er particle and were
analyzed for their N-terminal amino acid sequences (21).
Furthermore, we recently sequenced a 20-kbp chromosomal fragment of
E. carotovora subsp. carotovora Er which contained the open reading frames coding for the major sheath protein
(50 kDa), the major core protein (19 kDa), and the tail fiber protein
(68 kDa) (DDBJ nucleotide sequence accession no. AB017338). The
20-kbp fragment also contained the structural genes for the proteins of
46, 44, and 35 kDa, which might be the proteins for the antenna-like
and the base plate structures. Thus, carotovoricin Er is a
phage-tail-like bacteriocin consisting of at least six proteins.
A previous paper from our laboratory has shown that carotovoricin Er
binds to and kills several strains of E. carotovora subsp. carotovora, such as strains EC-2, P7, and 645Ar
(14). However, our recent experiments showed that (i) a
significant portion of the purified carotovoricin Er preparations
failed to bind to EC-2 and P7 but that almost all carotovoricin Er
particles bound to strain 645Ar under similar conditions and (ii) the
unbound fraction of carotovoricin Er recovered after the incubation
with EC-2 or P7 retained intact morphology and killing activity towards
P7 or EC-2, respectively (unpublished data). These results prompted us
to study whether or not the carotovoricin Er preparation contains multiple types of carotovoricin Er with different host specificities. In this paper, we show that E. carotovora subsp.
carotovora Er produces two types of carotovoricin Er with
different host specificities, which we named carotovoricin Era and Erb,
and that the different host specificities of carotovoricins Era and Erb
are due to alteration in the C-terminal part of the tail fiber protein
by a DNA inversion.
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MATERIALS AND METHODS |
Bacterial strains, plasmids, and culture media.
Bacterial
strains and plasmids used in this study are listed in Table
1. Bacteria were cultured in LB medium
(10 g of polypeptone, 5 g of yeast extract, and 5 g of
NaCl in 1 liter, pH 7.2) or in a modified M9 medium (14.7 g of
Na2HPO412H2O,
3 g of KH2PO4, 5 g of NaCl, 1 g of NH4Cl, 0.0147 g of
CaCl22H2O, 0.203 g of
MgSO4, 0.0002 g of
FeCl34H2O, and 2 g of
glucose in 1 liter, pH 7.2) supplemented with casein acid hydrolysate
(2 g/liter).
Assay for carotovoricin activity.
Test samples were serially
diluted with 0.05 M sodium phosphate buffer, pH 7.2. A small portion (5 µl) of the dilutions were withdrawn and spotted on an LB soft agar
plate (0.35% agar with a thickness of 2 mm) containing sensitive
bacteria (2 × 107 CFU/ml), and the plate
was incubated at 30°C for 8 to 12 h. The reciprocal of the
highest dilution that formed a clear zone in the LB soft agar was
defined as the relative killing titer (units) of carotovoricin.
Production and purification of carotovoricin Er and carotovoricin
CGE.
E. carotovora subsp.
carotovora strain Er or CGE234 M403 was grown in LB medium
at 30°C overnight. A portion (20 ml) of the culture was withdrawn,
transferred into 600 ml of the modified M9 medium, and cultivated for
several hours at 30°C. Mitomycin C (Wako Pure Chemical Industry,
Osaka, Japan) was added at a final concentration of 0.4 µg/ml to an
exponentially growing culture (with an optical density at 660 nm of
0.6), and the culture was incubated for a further 5 h at 30°C
with shaking to induce carotovoricin production accompanied by cell
lysis. Carotovoricin particles were purified from the cell lysates by a
purification procedure including the use of 15 to 30% (wt/vol) sucrose
linear gradient centrifugation in the presence of 20% (wt/vol) ethanol
and 0.1 M NaCl, as described previously (21).
Fixation of bacterial cells with formaldehyde.
Exponentially
growing cells of E. carotovora subsp.
carotovora in LB medium were collected by centrifugation at
2,500 × g at room temperature for 5 min. The cells
were suspended in LB medium and were treated with 2% formaldehyde at
room temperature for 60 min. After fixation, the cells were washed
twice with LB medium, and were suspended in LB medium at a
concentration of 1010 cells/ml.
Isolation of two types of carotovoricin Er.
Carotovoricin Er
particles were purified from the cell lysate of 2 liters of
E. carotovora subsp. carotovora Er as
described previously (21), and the carotovoricin Er
preparation was divided into two parts. One-half of the carotovoricin
Er preparation was mixed with 25 ml of formaldehyde-treated EC-2 cells,
and the rest was mixed with 25 ml of formaldehyde-fixed N786 cells. The
mixtures were rotated at room temperature for 30 min, followed by
centrifugation at 2,500 × g at room temperature for 10 min. The supernatants obtained were centrifuged at 120,000 × g at 4°C for 2 h, and carotovoricin Er particles in
the pellets were purified as described above (21).
Binding of carotovoricin Er to various strains of E.
carotovora subsp. carotovora.
Carotovoricin Er was incubated with formaldehyde-fixed cells
(500 µl) of E. carotovora subsp.
carotovora at 0°C for 1 h. The mixtures were
centrifuged at 12,000 × g at 0°C for 5 min to
collect bacterial cells. The supernatants obtained were centrifuged at 300,000 × g at 4°C for 2 h to collect unbound
carotovoricin particles.
SDS-PAGE and Western blotting.
SDS-PAGE was done as
described by Laemmli (18) using 12.5% acrylamide
gels. Proteins in the gel were electroblotted onto a polyvinylidene
difluoride sheet, and the blotted protein bands were immunostained with
specific antiserum raised against whole particles or the purified
sheath of carotovoricin Er. The immunostained bands were visualized
using alkaline phosphatase-conjugated anti-rabbit immunoglobulin G
(Promega, Madison, Wis.), nitroblue tetrazolium (Wako Pure Chemicals),
and 5-bromo-4-chloro-indolylphosphate (Wako Pure Chemicals). Antisera
were raised in female New Zealand White rabbits, which were injected
subcutaneously with the purified whole particle or sheath of
carotovoricin Er (1 mg) emulsified in Freund's complete adjuvant
(Difco Laboratories, Detroit, Mich.), followed by the injections of the
purified whole particle or sheath of carotovoricin Er (0.5 mg)
emulsified in Freund's incomplete adjuvant (Difco Laboratories) every
10 days for five times.
N-terminal amino acid sequences of proteins.
N-terminal
amino acid sequences of proteins were analyzed for the blotted protein
bands on a polyvinylidene difluoride sheet (19) by
using a model 491 protein sequencer (Perkin-Elmer Applied Biosystems,
Foster City, Calif.).
DNA manipulations.
All standard DNA manipulations were done
as described by Sambrook et al. (23). PCR was done using
Ex Taq polymerase (TaKaRa, Kyoto, Japan) for 30 cycles with
the following temperature profile: 94°C for 30 s, 57°C for
30 s, and 72°C for 3 min. Six primers for PCR were synthesized
according to the nucleotide sequence of the carotovoricin Er region of
E. carotovora subsp. carotovora Er
chromosome (DDBJ nucleotide sequence database accession no. AB017338).
Amplification of the DNA fragments containing invertible fragment
E by PCR and analysis of the PCR products.
The fragment
Er16098-17502, which contains invertible fragment E and a part of the
putative DNA invertase gene (Fig. 2), was amplified by PCR using
chromosomal DNA of strain Er as the template and the following
primers: 5'-AGCCGTGGGCGCGTATTTATAGCGATCAAG-3' (the forward
primer), corresponding to the DNA fragment from nucleotides 16098 to
16127, and 5'-AGCAGCATCGAGTCCGGCCCGTGTCCGTTC-3' (the reverse
primer), corresponding to the DNA fragment from nucleotides 17502 to
17473. Because a single NcoI site is contained in fragment E, cleavage of the amplified products at the NcoI site was
used for diagnosis of the DNA inversion of fragment E. The
amplified DNA fragments were digested with NcoI restriction
endonuclease and were then separated on a Tris-acetate-EDTA agarose gel
(1%). DNA fragments were extracted from the gel using Quantum
Prep Freeze 'N Squeeze DNA gel extraction spin columns (Bio-Rad
Laboratories, Hercules, Calif.). DNA sequencing was done using an ABI
Prism 373 DNA sequencer (Perkin-Elmer Applied Biosystems) and an ABI Prism Dye Terminator Cycle Sequencing Ready Reaction kit (Perkin-Elmer Applied Biosystems).
DNA inversion of segment E in Escherichia
coli.
The invertible segment E and the invertase gene
ein were separately cloned in compatible plasmids and
transformed into E. coli DH5
to study DNA inversion
of segment E in E. coli cells. The DNA fragment
containing segment E (Er14307-17502) was amplified by PCR using the
chromosomal DNA of strain Er as the template. The following forward and
reverse primers were used:
5'-GATCTAGAATATTGGCCGCCTGAGCTACG-3' (the forward
primer, which corresponds to the DNA fragment from nucleotides 14307 to
14336 except in the italicized region, where 1 nucleotide was changed
to create an XbaI site) and
5'-AGAAGCTTCGAGTCCGGCCCGTGTCCGTTC-3' (the reverse
primer, which corresponds to the DNA fragment from nucleotides 17502 to
17473, where 2 nucleotides were changed to create a
HindIII site). The PCR product was digested with
XbaI and HindIII and inserted into plasmid
pACYC184 (3). The recombinant plasmid was transformed into
E. coli DH5
(8). The presence of Ea and
Eb was assayed for single colonies of the resultant transformants by a PCR amplification of the Er16098-17502 fragment, followed by NcoI digestion and agarose gel electrophoresis
as described above. The DNA fragment containing the ein gene
(Er16993-17739) was amplified by PCR using the chromosomal DNA of
strain Er as the template. The following forward and reverse primers
were used: 5'-CGGAGTTGCTTGCGGCCATGGTAA-3' (the
forward primer, which corresponds to the DNA fragment from nucleotides
16993 to 17016; the italicized region indicates the NcoI
site) and 5'-ACCAAGCTTCTGGTCACTCTGGCGCAGAGG-3' (the reverse primer, which corresponds to the DNA fragment
from nucleotides 17739 to 17710, where 2 nucleotides were changed to create a HindIII site). The PCR products containing the
ein gene were digested with NcoI and
HindIII and cloned into the pTrc99A plasmid
to construct plasmid pTrc99Aein.
pTrc99Aein was transformed into E. coli DH5
harboring either pACYC184Ea or pACYC184Eb. The presence of Ea and Eb in the resultant transformants was assayed as
described as above.
Expression of the tail fiber genes of carotovoricins Era and Erb
in E. carotovora subsp. carotovora
strain CGE234 M403.
The DNA fragment containing the tail fiber
gene of carotovoricin Era or Erb was amplified by PCR using the
chromosomal DNA of strain Er as the template. To amplify the DNA
fragment containing the tail fiber gene of carotovoricin Era
(fibA), the following primers were used:
5'-GATCTAGAATATTGGCCGCCTGAGCTACG-3' (the forward primer, which is the same oligonucleotide as that described above for
amplification of segment E) and
5'-ATAAGCTTACCATGGCCGCAAGCAACTCCG-3' (the reverse
primer, which corresponds to the DNA fragment from nucleotides 17022 to
16993, where 2 nucleotides were changed to create a
HindIII site). To amplify the DNA fragment containing the tail fiber gene of carotovoricin Erb (fibB), we used a
reverse primer
(5'-GGTAAGCTTTTGGGATTTAATCACTGTGCC-3', which
corresponds to the DNA fragment from nucleotides 16586 to 16557 except
in the italicized region, where 2 nucleotides were changed to create a
HindIII site) in a combination with the same forward
primer used for amplification of the tail fiber gene of carotovoricin Era (fibA). The PCR products were digested with
XbaI and HindIII and were inserted into
pTrc99A plasmids to construct plasmids pTrc99AfibA and
pTrc99AfibB, respectively.
pTrc99AfibA and pTrc99AfibB were transformed into strain CGE234 M403. Production of carotovoricin CGE by the transformants was induced with mitomycin C, and normal and
hybrid carotovoricin CGE particles were purified as described previously (21).
 |
RESULTS AND DISCUSSION |
E. carotovora subsp. carotovora
Er produces two types of carotovoricin Er.
Carotovoricin Er was
purified from the lysate of mitomycin C-treated E. carotovora subsp. carotovora Er as described previously (21) and was assayed for its bactericidal activity towards
various strains of E. carotovora subsp.
carotovora (strains Er, 645Ar, EC-2, N786, and P7). The
carotovoricin Er preparation exhibited killing activity towards all of
the tested strains except towards the producing strain Er, although the
bactericidal titer of the carotovoricin Er preparation varied with
different strains (Table 2). To study
whether or not there exist multiple types of carotovoricin Er, the
killing spectrum of the carotovoricin Er preparation was assayed after
incubation with formaldehyde-treated cells of strain Er, 645Ar, EC-2,
N786, or P7 at 30°C for 30 min. When the carotovoricin Er preparation
was preincubated with the formaldehyde-fixed cells of strain EC-2, the
preparation lost the ability to kill 645Ar and EC-2 but it retained the
ability to kill N786 and P7 (Table 2). In contrast, the carotovoricin
Er preparation which was preincubated with fixed cells of N786 or P7
killed 645Ar and EC-2 but failed to kill N786 and P7 (Table 2). The
residual bactericidal activity of the carotovoricin Er preparation
which was recovered after incubation with fixed cells of EC-2 or N786
was abolished by further incubation with N786 or EC-2, respectively
(data not shown). These results suggested that the carotovoricin Er
preparations contained two types of carotovoricin Er with different
host range specificities.
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TABLE 2.
Bactericidal spectra of carotovoricin Er
preparations after incubation with various strains of E. carotovora subsp. carotovoraa
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To isolate different types of carotovoricin Er, a partially purified
preparation of carotovoricin Er was incubated with a
large number of
formaldehyde-treated cells of strain EC-2, N786,
or P7 at 30°C for 30 min, followed by centrifugation at 12,000
×
g for 5 min. Carotovoricin Er particles recovered from the supernatants
were
further purified by a procedure including the use of sucrose
density
gradient centrifugation in the presence of 20% (vol/vol)
ethanol as
described in Materials and Methods. Purified carotovoricin
Er was
analyzed for its protein components by using SDS-PAGE.
When the
partially purified preparation of carotovoricin Er was
further purified
after incubation with strain N786, it exhibited
three major protein
bands corresponding to 68, 50, and 19 kDa
on SDS-PAGE (Fig.
1A, lane 1). These results were
consistent with
our previous results showing that the tail fiber,
sheath, and
inner core of carotovoricin Er consisted of major proteins
of
68, 50, and 19 kDa, respectively (
21). Similar results
were
obtained when the carotovoricin Er preparation was incubated with
strain P7 instead of strain N786 (data not shown). In contrast,
when
the carotovoricin Er preparation was purified after incubation
with
strain EC-2, purified carotovoricin Er gave three major protein
bands
corresponding to 76, 50, and 19 kDa but no intense band
corresponding
to 68 kDa (Fig.
1A, lane 2). The protein band corresponding
to 76 kDa
was also detected for the carotovoricin Er preparation
before the
incubation with strain N786, P7, or EC-2, although
it was 1/5 to 1/10
less intense than the band corresponding to
68 kDa (Fig.
1A, lane 3).
Protein bands of purified carotovoricin
Er (Fig.
1A, lanes 1 and 2)
were blotted onto a polyvinylidene
difluoride sheet and were analyzed
for their N-terminal amino
acid sequences. We found that (i) the 11 N-terminal residues of
the 76-kDa protein (i.e.,
Ala-Asn-Leu-Ser-Glu-Asn-Pro-Gln-Trp-Val-Asp-)
were identical to those
of the 68-kDa tail fiber protein and (ii)
the other major proteins of
68, 50, and 19 kDa had N-terminal
amino acid sequences identical to
those of the purified tail fiber,
sheath, and inner core,
respectively. These results showed that
E. carotovora subsp.
carotovora Er produces two types of
carotovoricin
Er with identical sheath and core parts but different
tail fiber
proteins with identical N-terminal regions. Two types of
carotovoricin
Er exhibiting the protein bands corresponding to 68 and
76 kDa
on SDS-PAGE were designated carotovoricin Era and Erb,
respectively.
Carotovoricin Era and Erb were tested for their abilities
to bind
to and kill strains 645Ar, EC-2, N786, and P7, as described in
Materials and Methods. As shown in Fig.
1B, carotovoricin Era
bound to
and killed strains 645Ar and EC-2 (lanes 2 and 3) but
it did not bind
to Er, N786, or P7 (lanes 1, 4, and 5). In contrast,
carotovoricin Erb
exhibited the ability to bind to and kill N786
and P7 (Fig.
1B, lanes 9 and 10) but not Er and EC-2 (Fig.
1B,
lanes 6 and 8). The results
indicated that carotovoricin Era and
Erb have different host
specificities, probably due to their different
tail fiber proteins.

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FIG. 1.
Major components of two types of carotovoricin Er (A)
and binding of carotovoricin Era and Erb to various strains of
E. carotovora subsp. carotovora (B).
(A) A portion of a carotovoricin Er preparation was incubated with a
large number of formaldehyde-fixed cells of strain N786 (lane 1) or
EC-2 (lane 2), followed by centrifugation at 2,500 × g at room temperature for 10 min. Carotovoricin
particles were purified from the supernatants as described in Materials
and Methods, and 10 µg of protein from the purified carotovoricin
preparation was loaded onto an SDS-12.5% polyacrylamide gel.
For comparison, the carotovoricin Er preparation before the incubation
with strain N786 or EC-2 was also loaded onto the same gel (lane 3).
(B) Purified carotovoricin Era (Fig. 1A, lane 1) or Erb (Fig. 1A, lane
2) was incubated with formaldehyde-fixed cells of various strains at
0°C for 60 min. After centrifugation at 2,500 × g at 0°C for 10 min, the precipitates (the bacterial
cells) and the supernatants obtained were subjected to Western blotting
using antisheath antiserum, as described in Materials and Methods. The
results of killing of various strains by carotovoricin Era or Erb were
from Table 2. Ctv, carotovoricin. +, killed. , not killed.
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Carotovoricin Era and Erb failed to bind to the strain that produced
them, Er (Fig.
1B), implying that the resistance of strain
Er to the
bacteriocin is not due to the presence of an immunity
system but is due
to the lack of a receptor(s) for carotovoricin
Er. It was also noted
that carotovoricin Era and Erb bound to
strain 645Ar but that only
carotovoricin Era killed the strain
(Fig.
1B). It will be interesting
to study whether strain 645Ar
has two different receptors for two
types of carotovoricin Er.
It also remains to be studied whether
carotovoricin Er utilizes
lipopolysaccharide of
E. carotovora subsp.
carotovora as the receptor.
Pyocin R
was shown to bind to lipopolysaccharide of the host bacterium
(
11).
A DNA inversion in the tail fiber gene is responsible for the
production of two types of carotovoricin Er.
It has been
demonstrated that bacteriophages Mu and P1 alter the C-terminal regions
of tail fiber proteins by DNA inversion, leading to alteration of their
host range (5, 6, 10, 17, 24, 28). Since two properly
oriented recombination sites (inverted repeats), a DNA invertase, and a
recombinational enhancer are essential for a DNA inversion system
(15), we searched the corresponding sequences on the
20-kbp fragment from the E. carotovora subsp. carotovora Er chromosome (DDBJ nucleotide sequence database
accession no. AB017338), which includes the genes encoding the major proteins of the sheath, core, and tail fiber of carotovoricin Er. As
illustrated in Fig. 2, (i) the 20-kbp
fragment contains a pair of 26-bp inverted-repeat sequences which are
located inside and downstream of the gene encoding the tail fiber
protein of 68 kDa; (ii) the inverted repeats flank a 790-bp segment, or
the putative invertible segment, which covers the region corresponding to the C-terminal part of the tail fiber protein; (iii) a segment corresponding to a DNA invertase gene is located immediately
downstream of the 790-bp segment; and (iv) the putative DNA invertase
gene contains a recombinational-enhancer-like segment in its 5'
region (Fig. 2).

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FIG. 2.
Tail fiber gene of carotovoricin Er and a possible DNA
inversion system in the 20-kbp carotovoricin Er region of
E. carotovora subsp. carotovora Er.
Invertible segment E is illustrated in the same (A) or in the reverse
(B) direction compared to that of the nucleotide sequence registered in
the DDBJ nucleotide sequence database (accession no. AB017338), and the
corresponding E fragment is designated Ea or Eb, respectively.
Invertible segment E is flanked by the left inverted-repeat sequence
(filled triangle) and by the right inverted-repeat sequence (open
triangle). fibA and fibB are the tail
fiber genes with a part of Ea and Eb, respectively. A putative DNA
invertase gene, ein, is located directly to the right of
E, and it contains a recombinational enhancer (hatched box) at
the 5' terminus. Nucleotides (nt) 16098 and 17502 are the
nucleotide numbers of the 20-kbp carotovoricin Er region registered in
the DDBJ nucleotide database (accession no. AB017338).
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The invertible segments in the previously reported DNA inversion
systems were designated H for the phase variation in
Salmonella enterica serovar Typhimurium (
29), G in bacteriophage
Mu (
5,
17,
28), C in bacteriophage P1 (
10),
and P in the
E. coli chromosomal element e4
(
22), and the corresponding DNA invertases
were Hin, Gin,
Cin, and Pin, respectively. The invertible 790-bp
segment was
designated E (for carotovoricin Er), and the E segments
with forward
and reverse orientations registered in the DDBJ nucleotide
sequence database were referred to as Ea and Eb, respectively
(Fig.
2).
The putative DNA invertase for E was designated Ein.
Based on the
alignment of the 26-bp inverted repeats for Ein with
those for Gin
(
22), Cin (
9), Hin (
30), and Pin
(
22) (data
not shown), we defined a consensus sequence of
the inverted repeats
for the DNA invertases as follows:
5'-TT-TC-AAACCT-GGTTT-GAGAA-3',
where at least 7 of 10 inverted repeats have the same nucleotide
in each position. The left
inverted repeat for Ein (i.e.,
5'-CTCCCGCAAACCTCGGTTTTGGGGAC-3')
displayed identity in 16 of the 20 nucleotides of the consensus
sequence, and the right inverted
repeat for Ein (i.e., 5'-TTCTCGCAAACCTCGGTTTTGGAGAA-3')
was
identical with the consensus sequence. Alignment of the deduced
amino
acid sequence for Ein with those for Gin, Cin, Hin, and
Pin (
9,
22,
30) indicated that there was a considerable
degree of
identity between the amino acid residues of Ein and
the other DNA
invertases, ranging from 61 to 67% (data not shown).
Interestingly,
many differences in the DNA sequence were found
in the third nucleotide
of codons, leaving the amino acid sequences
unaltered. This implies a
selective pressure to keep the protein
functional. The 90-bp segments
of the recombinational enhancer
within
ein showed more than
60% identity to those of the other
DNA invertase genes (data not
shown). Thus, the existence of a
DNA inversion system for production of
two types of carotovoricin
Er was strongly suggested, and inversion of
segment E would lead
to the production of two different tail fiber
proteins with identical
N-terminal
regions.
To demonstrate the occurrence of DNA inversion in
E. carotovora subsp.
carotovora Er, we attempted to detect
the Ea and Eb
segments in the Er16098-17502 region of the bactrial
chromosome
(Fig.
2). The Ea-containing fragment
(Era16098-17502) included
a single
NcoI site (DDBJ
nucleotide sequence database accession
no.
AB017338), which, when
cleaved, would divide the 1,403-bp
fragment into two segments of
approximately 900 and 500 bp (Fig.
3A).
In contrast, the Eb-containing fragment (Erb16098-17502)
would be
cleaved by
NcoI into two fragments of approximately 1,200
and 200 bp (Fig.
3A). The fragment corresponding to Er16098-17502
was
amplified by a PCR using chromosomal DNA of strain Er as the
template,
as described in Materials and Methods. The amplified
products were
digested by
NcoI and were loaded onto an agarose
gel. The
NcoI digestion of the fragment produced five DNA bands
corresponding to approximately 1,400, 1,200, 900, 500, and 200
bp (Fig.
3B). Sequencing of the fragments showed that the fragments
of 900 and
500 bp were derived from
NcoI-digested Era16098-17502,
while
the segments of 1,200 and 200 bp were from
NcoI-digested
Erb16098-17502. Similar results were obtained when fresh single
colonies (
n = 20) of strain Er were used as the source
of the
DNA template for the amplification of the Er16098-17502 fragment
by PCR (data not shown). These results indicated that the E fragment
was invertible in vivo. The tail fiber genes containing Ea and
Eb were
designated
fibA and
fibB, respectively. The open
reading
frames for FibA and FibB comprised 2,001 bp and 2,142 bp,
respectively,
coding for 666 and 713 amino acid residues. Calculated
molecular
masses were 70,792 and 75,910 Da for FibA and FibB,
respectively,
and they shared identical 568-residue polypeptides from
the N
termini. Thus, the DNA inversion changed the C-terminal one-fifth
portion of the tail fiber protein of carotovoricin Er.

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FIG. 3.
Existence of the invertible segments Ea and Eb in the
chromosome of E. carotovora subsp.
carotovora Er. (A) The 1,403-bp DNA fragments containing
the putative invertible segments Ea and Eb (from nucleotides [nt]
16098 to 17502; see also Fig. 2) are illustrated. Filled arrows in the
upward direction indicate the NcoI sites, which divide
the 1,403-bp fragments containing Ea or Eb into 900- and 500-bp
fragments or 200- and 1,200-bp fragments, respectively. Nucleotides
16098 and 17502 are the nucleotide numbers of the 20-kbp carotovoricin
Er region registered in the DDBJ nucleotide database (accession no.
AB017338). (B) The 1,403-bp DNA fragments were amplified by PCR using
the chromosomal DNA of E. carotovora subsp.
carotovora Er as the template. The PCR products obtained
were digested with NcoI restriction endonuclease and
were separated on a 1% agarose gel. Lane 1, size markers; lane 2, NcoI digests of the amplified DNA fragments from
nucleotides 16098 to 17502.
|
|
Furthermore, the function of
ein was tested using an
E. coli system where invertible segment E and the
ein gene were separately
carried by compatible plasmids; the
DNA fragment containing segment
E (Er14307-17502) and the DNA fragment
containing the
ein gene
(Er16993-17739) were amplified by
PCR using the chromosomal DNA
of strain Er as the template and were
cloned into pACYC184 and
p
Trc99A, respectively. After
transformation of
E. coli DH5

with
the recombinant
plasmid(s), the Ea and the Eb fragments in the
transformants were
detected by an amplification of the Er16098-17502
fragments by PCR,
followed by
NcoI digestion and agarose gel electrophoresis
as described above. Single colonies (
n = 20) of the
transformants
harboring only recombinant pACYC184 gave either a
combination
of 900- and 500-bp fragments or a combination of 1,200- and
200-bp
fragments (data not shown). However, when
E. coli DH5

carrying
pACYC184Ea or pACYC184Eb (i.e.,
pACYC184 containing Ea or Eb)
was further transformed with
p
Trc99A
ein (i.e., p
Trc99A containing
ein), the resultant transformants gave the bands
corresponding
to 1,200, 900, 500, and 200 bp (data not shown). These
results
indicated that the function of
ein was necessary for
DNA inversion
of segment E and that the DNA inversion took place in the
forward
and backward
directions.
Tail fiber proteins determine the host range specificity of
carotovoricin.
To study if the tail fiber proteins determine the
host specificity of carotovoricin Er, we expressed the tail fiber gene
fibA or fibB in E. carotovora
subsp. carotovora CGE234 M403 to produce hybrid
carotovoricin CGE possessing FibA or FibB and tested the host
specificity for the hybrid carotovoricins. E. carotovora subsp. carotovora CGE234 M403 is
nonpathogenic to plants but retains bactericidal activity towards the
same bacterial species, probably because of its ability to produce two
types of bacteriocin, high-molecular-weight and low-molecular-weight
bacteriocins (4, 25). In this study, we purified the
high-molecular-weight bacteriocin from the mitomycin C-treated cells of
strain CGE234 M403 according to the procedure for purification of
carotovoricin Er (21). Electron microscopy of the purified
high-molecular-weight bacteriocin showed the same phage-tail-like
morphology as that of carotovoricin Er (data not shown). SDS-PAGE for
the purified bacteriocin indicated major protein bands corresponding to
84, 70, 64, 55, 50, and 19 kDa (Fig. 4A).
The 20 N-terminal amino acid residues of the 50- and the 19-kDa
proteins were 100% identical to those of the sheath and the core
proteins of carotovoricin Er, respectively. Furthermore, the 15 N-terminal amino acid residues of the 64-kDa protein (i.e., Ala-Asn-Leu-Ser-Glu-Asn-Pro-Gln-Trp-Val-Asp-Ser-Ile-Tyr-Gln-) were identical
with those of the tail fiber protein of carotovoricin Er, except for
Ser in the 12th position (i.e., the tail fiber proteins of
carotovoricin Er, FibA and FibB, have Gly for Ser in the same
position). However, the 64-kDa protein was not immunostained with the
antiserum raised against carotovoricin Er (Fig. 4B), implying that the
C-terminal region of the 64-kDa protein is different from those of
carotovoricin Era and Erb. Based on these results, the
high-molecular-weight bacteriocin from strain CGE234 M403 was
designated carotovoricin CGE and we determined that carotovoricin CGE
has a structure similar to that of carotovoricin Er except for the tail
fiber protein, implying that the tail fiber protein of carotovoricin
CGE might be interchangeable with those of carotovoricin Er. Since
Western blotting of purified carotovoricin CGE using antiserum against
carotovoricin Er revealed a prominent band corresponding to 55 kDa
(Fig. 4B), we determined the amino acid sequence for the 11 N-terminal
residues of the 55-kDa protein:
Ala-Asn-Leu-Ser-Glu-Gln-Glu-Ser-Trp-Ile-Asp-. The 5 N-terminal amino
acid residues of the 55-kDa protein are identical to those of the tail
fiber protein of carotovoricin CGE, but the rest of the amino acid
residues are different from those of the tail fiber protein.
Furthermore, an open reading frame coding for the 64-kDa protein is
present in the 20-kbp carotovoricin CGE region of strain CGE234 M403,
while no open reading frame for the 55-kDa protein is present in the
same region (M. Hirota et al., unpublished results). Therefore,
the 64-kDa protein may be the major tail fiber protein of carotovoricin
CGE, but it remains unclear if the 55-kDa protein is a structural
component of carotovoricin CGE.

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FIG. 4.
SDS-PAGE (A) and Western blotting (B) for the purified
carotovoricin CGE. (A) Purified carotovoricin CGE (15 µg of
protein) was electrophoresed in an SDS-polyacrylamide gel. The protein
bands were stained with Coomassie brilliant blue R-250. For comparison,
purified carotovoricin Er (20 µg of protein) was also electrophoresed
in the same gel. (B) Purified carotovoricin CGE (3 µg of protein) and
carotovoricin Er (4 µg of protein) were subjected to SDS-PAGE,
followed by Western blotting using specific antiserum raised against
purified carotovoricin Er as described in Materials and Methods. Note
that the antiserum did not stain the 64-kDa tail fiber protein of
carotovoricin CGE. CGE, carotovoricin CGE; Er, carotovoricin Er.
|
|
Carotovoricin CGE exhibited no ability to kill strains Er, 645Ar, EC-2,
N786, and P7 (Fig.
5A), indicating that
carotovoricin
CGE has a host specificity different from that of
carotovoricin
Er, possibly due to a different C-terminal region of the
tail
fiber protein. To produce hybrid carotovoricin CGE with the
corresponding
tail fiber protein, strain CGE234 M403 was transformed
with the
multicopy vector p
Trc99A carrying
fibA
or
fibB. Carotovoricin
particles were purified from the
lysate of the mitomycin C-treated
transformants and were analyzed
for bactericidal activity towards
various indicator strains. As
shown in Fig.
5A, the purified carotovoricin
preparation from the
transformant harboring p
Trc99A
fibA killed
strains
645Ar, EC-2, and T-29 (the indicator strain for carotovoricin
CGE) but did not kill strains N786 and P7. In contrast, carotovoricin
preparation from the transformant harboring
p
Trc99A
fibB exhibited
activity bactericidal to
strains N786, P7, and T-29 but no ability
to kill strains 645Ar
and EC-2 (Fig.
5A). Carotovoricin preparations
from all of the
transformants killed strain T-29 (Fig.
5A), indicating
that normal
carotovoricin CGE was also produced by the transformants.
SDS-PAGE
indicated that the transformants carrying plasmid
p
Trc99A
fibA or p
Trc99A
fibB
produced carotovoricins possessing a 68- or 76-kDa
protein,
respectively (Fig.
5B, lanes 3 and 4). Furthermore, Western
blotting
using antiserum specific to purified carotovoricin Er
showed that FibA
(68 kDa) or FibB (76 kDa) protein was present
in the carotovoricin
preparation obtained from the transformant
carrying
p
Trc99A
fibA or p
Trc99A
fibB,
respectively (Fig.
5C, lanes
3 and 4). These results showed that the
transformants carrying
p
Trc99A
fibA or
p
Trc99A
fibB produced hybrid carotovoricin CGE
possessing
FibA or FibB, respectively, and that the tail fiber
proteins,
more specifically their C-terminal parts, determined host
range
specificity. It has been demonstrated that in many of the
well-known
tailed bacteriophages, such as

, P1, Mu, and T4, the
N-terminal
part of tail fiber proteins is bound to the base plate or to
the
tail shaft and the C-terminal part is the distal part that binds
to
a specific receptor (
2,
20). In Mu and P1 phages, DNA
inversion of segments G and C results in the formation of tail
fiber
proteins with a constant N-terminal part and two alternative
C-terminal
parts, alternating the host range specificities of
the phages. With
these results taken together, it is quite conceivable
that the host
range specificity of carotovoricin Er is determined
by the C-terminal
part of the tail fiber protein. The production
of carotovoricins aid
E. carotovora subsp.
carotovora in surviving
competition among the same and closely related species of bacteria
in
nature, and alteration in the C-terminal part of tail fiber
proteins by
DNA inversion is an effective way to furnish carotovoricin
with a wider
bactericidal spectrum.

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FIG. 5.
Killing spectra of the transformants of E.
carotovora subsp. carotovora CGE234 M403
carrying fibA or fibB (A) and production
of hybrid carotovoricin CGE possessing FibA or FibB (B and C). The tail
fiber genes of carotovoricin Era and Erb (fibA and
fibB, respectively) were expressed in
E. carotovora subsp. carotovora
strain CGE234 M403, and carotovoricin particles were purified and
analyzed as described in Materials and Methods. (A) Purified
carotovoricins from the transformants carrying pTrc99A,
pTrc99AfibA, or
pTrc99AfibB were spotted on an LB
soft agar plate containing E. carotovora subsp.
carotovora strain 645Ar, EC-2, N786, P7, or T-29,
and a clear zone was observed after incubation at 30°C for 8 to
12 h. (B) Purified carotovoricin particles (15 µg of protein)
from the transformants carrying pTrc99A,
pTrc99AfibA, or
pTrc99AfibB were electrophoresed in an
SDS-polyacrylamide gel (lane 2, 3, or 4, respectively). The
protein bands were stained with Coomassie brilliant blue R-250
(CBB). Purified carotovoricin Er (12 µg of protein) was also
electrophoresed in the same gel (lane 1). (C) Purified
carotovoricin particles (3 µg of protein) from the transformants
carrying pTrc99A,
pTrc99AfibA, or
pTrc99AfibB were subjected to SDS-PAGE,
followed by Western blotting using a specific antiserum against
carotovoricin Er (lane 2, 3, or 4, respectively). Lane 1, purified
carotovoricin Er (3 µg of protein).
|
|
 |
ACKNOWLEDGMENTS |
We thank Elisabeth Hofstad for her help in the preparation of the manuscript.
This work was supported in part by a grant-in-aid for scientific
research from the Ministry of Education, Science, Sports and Culture of
Japan. H. A. Nguyen was the recipient of a Japanese government
scholarship from the Ministry of Education, Science, Sports, and
Culture of Japan.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan. Phone:
81(22)717-8779. Fax: 81(22)717-8780. E-mail:
ykamio{at}biochem.tohoku.ac.jp.
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Journal of Bacteriology, November 2001, p. 6274-6281, Vol. 183, No. 21
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.21.6274-6281.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
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