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Applied and Environmental Microbiology, May 2001, p. 2062-2069, Vol. 67, No. 5
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.5.2062-2069.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Sequence Analysis of Insecticidal Genes from
Xenorhabdus nematophilus PMFI296
J. Alun W.
Morgan,1,*
Martin
Sergeant,1
Debbie
Ellis,2
Margaret
Ousley,1 and
Paul
Jarrett2
Department of Plant Pathology and
Microbiology1 and Department of
Entomological Sciences,2 Horticulture
Research International, Wellesbourne, Warwick CV35 9EF, United Kingdom
Received 18 October 2000/Accepted 12 February 2001
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ABSTRACT |
Three strains of Xenorhabdus nematophilus showed
insecticidal activity when fed to Pieris brassicae (cabbage
white butterfly) larvae. From one of these strains (X. nematophilus PMFI296) a cosmid genome library was prepared in
Escherichia coli and screened for oral insecticidal
activity. Two overlapping cosmid clones were shown to encode
insecticidal proteins, which had activity when expressed in E. coli (50% lethal concentration [LC50] of 2 to 6 µg of total protein/g of diet). The complete sequence of one cosmid
(cHRIM1) was obtained. On cHRIM1, five genes (xptA1, -A2, -B1,
-C1, and -D1) showed homology with up to 49%
identity to insecticidal toxins identified in Photorhabdus
luminescens, and also a smaller gene (chi) showed
homology to a putative chitinase gene (38% identity). Transposon
mutagenesis of the cosmid insert indicated that the genes xptA2,
xptD1, and chi were not important for the expression
of insecticidal activity toward P. brassicae. One gene
(xptA1) was found to be central for the expression of activity, and the genes xptB1 and xptC1 were
needed for full activity. The location of these genes together on the
chromosome and therefore present on a single cosmid insert probably
accounted for the detection of insecticidal activity in this E. coli clone. Although multiple genes may be needed for full
activity, E. coli cells expressing the xptA1
gene from the bacteriophage lambda PL promoter
were shown to have insecticidal activity (LC50 of 112 µg
of total protein/g of diet). This is contrary to the toxin genes
identified in P. luminescens, which were not insecticidal
when expressed individually in E. coli. High-level gene
expression and the use of a sensitive insect may have aided in the
detection of insecticidal activity in the E. coli clone
expressing xptA1. The location of these toxin genes and the
chitinase gene and the presence of mobile elements (insertion sequence)
and tRNA genes on cHRIM1 indicates that this region of DNA represents a
pathogenicity island on the genome of X. nematophilus PMFI296.
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INTRODUCTION |
Currently, the most successful
microbial insecticide is based on the bacterium Bacillus
thuringiensis (16, 21) that produces insecticidal
crystalline toxins during sporulation (20). The recent use
of B. thuringiensis on a large scale and the development and
use of transgenic plants expressing these toxin genes (3, 23) may enhance the development of resistant insect populations. New protein toxins are therefore required to provide a greater diversity of genes for use in pest control (14, 15, 31).
In the search for new genes, we have identified, by testing
nonluminescent bacterial strains (Xenorhabdus species)
isolated from insect parasitic nematodes (IPNs) for their ability to
kill insects, a group of orally active protein toxins
(22). Both IPNs and even their associated bacteria and
toxins when injected into the insect hemocoel are well known for their
ability to kill insects (2, 4, 12, 27, 32, 33). These
properties are important for pathogenicity; however, for exploitation a
toxin that is active when fed to insects is important. Ensign et al. (13) have identified protein toxins from the bacterium
Photorhabdus luminescens with oral insecticidal activity
which have been studied in detail (8, 9, 13, 18). However,
when the toxin genes from P. luminescens were cloned and
expressed in Escherichia coli they did not display
insecticidal activity (9). Since both Xenorhabdus and Photorhabdus spp. cannot survive
in water or soil for long, their use as a biopesticide may be limited.
It is therefore important that the toxicity detected in these bacteria
can be genetically moved to other bacteria, microorganisms, or plants for their exploitation. To enable this and to study the toxins in
greater detail, the ability to express these proteins in a heterologous host and maintain their insecticidal activity is essential. We describe here the discovery of a strain of X. nematophilus and the isolation of an E. coli clone
expressing a region of its genomic DNA which, when fed to Pieris
brassicae larvae, causes a rapid cessation in feeding and
mortality. The sequence of the insert and the identification of the
genes involved in insecticidal activity are presented.
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MATERIALS AND METHODS |
Bacterial strains and media.
A strain of X. nematophilus 9965 was obtained from the NCIMB culture collection,
Aberdeen, United Kingdom. Strains X. bovenii (UQM2872),
X. beddingii (UQM2211), X. poinarii (ATCC 4921),
and X. redingi were a gift from Noel Boemare,
INRA-CNRS, Paris, France. The other Xenorhabdus strains were
isolated from infective nematodes present in United Kingdom soil by
using an insect entrapment method (4). Samples of
hemolymph containing characteristic rod-shaped bacteria were plated
onto NBTA (1) composed of nutrient agar (NA; Difco,
Detroit, Mich.) containing bromophenol blue (25 mg liter
1) and triphenyl 235 tetrazolium chloride (4 mg
liter
1) and incubated at 25°C for 72 h. Plates
where the bacterial colonies were dark blue were subcultured on NBTA
and incubated at 25°C for 72 h to ensure purity. Nonluminescent
strains were presumptively identified as Xenorhabdus species
and used in this work. The strains were routinely maintained on NA.
Insect bioassay.
The insecticidal activity of bacterial
isolates was tested with neonate P. brassicae larvae.
Individual colonies were cultured in Luria broth (LB; Difco) at 28°C
for 18 h at 200 rpm. A 50-µl sample was spread onto an
agar-based artificial diet (11) which contained
streptomycin (20 µg ml
1) and cefataxime and
tetracycline (each at 100 µg ml
1). To each container
(4.5 cm in diameter), 10 larvae were added, and the assay pots were
incubated at 25°C (16-h day length period), with a relative humidity
of 80% for 96 h. Daily recordings of larval mortality and the
size of the surviving larvae were made. Insecticidal strains were
selected when reduced larval size was observed and >50% of the
insects had been killed.
The potency of active bacteria was tested using a multidose
incorporation assay. Assays were performed with a series of five dilutions of the original cultures made in phosphate-buffered saline
(0.05 mM phosphate buffer with 0.125 M NaCl) using a minimum of 40 larvae per concentration. Assays were incubated at 25°C, with a
relative humidity of 80%, for 6 days with a 16-h day length period.
The mortality was recorded, and the 50% lethal concentration (LC50) was determined by probit analysis (17).
In the assays, negative controls included treatments with just water
and with E. coli. The protein concentration of samples was
determined using the BCA reagent kit (Pierce).
Strain characterization.
PCR amplification of DNA was
performed on purified DNA using an Omnigene Thermocycler (Hybaid,
Teddington, United Kingdom). DNA was isolated from bacterial cultures
grown at 30°C for 18 h on NA using a Qiagen kit (Qiagen,
Dorking, United Kingdom). A loopful of each culture was resuspended in
1 ml of buffer B1; to this, 0.35 ml of buffer B2 and 0.4-g glass beads
(0.1 mm in diameter) were added. The sample was vortexed at maximum
speed for 10 min and centrifuged at 13,000 × g for 5 min. The supernatant was applied to the top of a Qiawell 8 column
(Qiagen), and the DNA was purified according to the manufacturer's
instructions. After ethanol precipitation the sample was resuspended in
100 µl of 1 mM Tris-HCl (pH 8). To a 100-µl PCR reaction, 4 to 20 µl of DNA was added. The reaction mix contained 1× buffer (Flowgen, Lichfield, United Kingdom), 100 pmol of each deoxynucleoside
triphosphate, 200 µmol of each primer, and 1 U of Dynazyme (Flowgen).
The samples were overlaid with 50 µl of mineral oil. For
amplification of the 16S rRNA gene, the primers
AAGGAGGTGATCCAGCCGCA and GGAGAGTTAGATCTTGGCTC were used (10). Following amplification, a 5-µl
aliquot was run on a standard 1% (wt/vol) agarose gel set at 100 V for
2.5 h to identify PCR products. The 16S rRNA gene PCR products (5 to 17 µl) were digested with the restriction enzymes AluI,
CfoI, DdeI, HaeI, HinfI,
RsaI, and Sau3A in a final volume of 20 µl in
1× buffer at 37°C for 3 h. All comparisons from a single digest were made on one gel to ensure the reliability of any comparisons.
Cloning of genomic DNA fragments encoding insecticidal
activity.
Total DNA was isolated from a culture of PMFI296 grown
in LB (Sigma, Poole, United Kingdom) at 28°C and 200 rpm to an
optical density of 1.5 (600 nm) using a genomic DNA
purification kit (Qiagen). Genomic DNA was partially digested with
Sau3A to give a dominant fragment size between 30 to 50 kb.
The genomic DNA was ligated to Supercos DNA (Stratagene,
Amsterdam, The Netherlands) cut with BamHI and
XbaI using standard procedures (25). The
ligated DNA was packaged (Stratagene) and transformed into E. coli DH5
cells. Any colonies that grew on LB agar supplemented
with 50 µg of kanamycin ml
1 at 30°C within 30 h
were tested for insecticidal activity by small-scale toxicity tests.
Subcloning was performed using standard techniques as outlined in the
appropriate sections.
DNA sequencing.
A system of subcloning larger fragments of
cHRIM1 in pUC19, designing new sequencing primers and walking out from
known sequences, and random sequencing of small EcoRV DNA
fragments of cHRIM1 in pUC19 was used to obtain the sequence of the
cosmid insert. All sequencing reactions were performed using the ABI
PRISM Dye Terminator Cycle Sequencing Ready Reaction Kit (Applied
Biosystems, Liverpool, United Kingdom) and analyzed on an automated DNA
sequencer (Applied Biosystems). Sequences were edited and assembled
using Sequencher 3.1 (Gene Codes Corp.) and DNA* (DNAStar, Inc.)
software. Sequence analysis was performed using the packages FASTA
(6.0), PILEUP (GCG), PLOTSIMILARITY (GCG), and the EBI internet system.
DNA mapping and translation were performed using the programs Clone Manager and Enhance (Scientific & Educational Software).
Transposon mutagenesis.
Transposon mutagenesis using
Tn3 was carried out essentially by the method of Seifert et
al. (30). cHRIM1 DNA was cut with PstI (sites
only within the cosmid) and cloned into the plasmid pBRMCS-2 cut with
NsiI to create plasmid pHRIM555 (kanamycin resistant). This
removed the ampicillin resistance gene from the cosmid and created a
mobilizable plasmid system. Plasmid pHRIM555 was transformed into
E. coli (pLBIO1) selecting for kanamycin and chloramphenicol resistance. The resulting strain was mated with E. coli
RDP146 (pOX38:mTn3-HIS3), and the cointegrates were resolved
by mating this strain with E. coli NS2115Sm and selection
with ampicillin, kanamycin, and streptomycin. Artificial transposon
mutagenesis was also carried out using the transposon AT2 on purified
DNA (Qiagen-Midi) following the manufacturer's protocols (Applied Biosystems). To locate the transposon insertion positions, plasmid DNA
was purified (Qiagen Qiawell 8 Miniprep), and the primers Tn3Pw3 (24) (TACTCATATATACTTTAGAT),
Tn3Pw6 (24) (ATACGCTCACGTACATGCTA), and AT2+ and AT2
(Applied Biosystems)
were used to sequence outward from the transposon ends.
SDS-PAGE of cell proteins.
X. nematophilus
PMFI296 was grown in 50 ml of LB at 30°C at 150 rpm for 2 days.
E. coli, E. coli (cHRIM1), and E. coli (clone 338) were grown at 30°C for 1 day in LB and LB containing 50 µg of
kanamycin or 20 µg of chloramphenicol ml
1,
respectively. The cell cultures were centrifuged at 10,000 × g for 15 min, and the cell pellet was washed twice with
phosphate-buffered (10 mM) saline (125 mM). The cells were disrupted by
three rounds of sonication (18 µ peak to peak for 30 s), and the cell
debris was removed by centrifugation at 13,000 × g for
15 min. Samples (5 µl) were analyzed by sodium dodecyl
sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) using a 3 to 8%
precast gradient gel (Novex, San Diego, Calif.) run at 150 V for
1.5 h. The gels were either stained with 0.25% (wt/vol) Coomassie
brilliant blue in 40% (vol/vol) methanol-10% (vol/vol) acetic acid
for 1 h and destained for 3 h or else stained for 45 min with
SYPRO Orange (Bio-Rad, Hemel Hampstead, United Kingdom) in 7.5%
(vol/vol) acetic acid. N'-terminal protein sequencing was performed on
peptides transferred to a polyvinylidene difluoride membrane after
SDS-PAGE using the manufacturer's recommended conditions (Novex).
Sequencing was carried out at the Protein Sequencing Service of the
Babraham Institute.
Induction of expression from PL
promoter.
High-level expression of proteins was achieved by
subcloning the xptA1 gene into the vector pLEX (Invitrogen,
Groningen, The Netherlands). E. coli and E. coli
carrying pHRIM801 were grown in RMG media (2% [wt/vol] amicase, 5%
[wt/vol] glucose, and 1 µM MgCl2 in M9 minimal salts
solution) containing ampicillin (50 µg ml
1), where
appropriate, at 30°C and 200 rpm for 18 h. An aliquot (1 ml) was
transferred to LB containing tryptophan (100 µg ml
1)
and, where appropriate, ampicillin (50 µg ml
1) to
induce expression from the bacteriophage lambda
PL promoter. After incubation at either 37 or
30°C, the cells were collected at various intervals by centrifugation
at 8,000 × g for 10 min. The cells were analyzed
directly by SDS-PAGE for the presence of a 280-kDa protein. A soluble
fraction and a fraction containing inclusion bodies were prepared as
outlined in Sambrook et al. (29), using sonication to
disrupt cells (three 30-s bursts at 18 µ peak to peak) and 50 mM
phosphate buffer (pH 7.2) containing 0.5 M urea to wash the inclusion
bodies. The two fractions (soluble and inclusion bodies) were analyzed
by SDS-PAGE.
Nucleotide sequence.
The complete sequence of the cosmid
cHRIM1 indicating the positions of genes described here has been
deposited in the EMBL database under accession number AJ308438.
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RESULTS |
Identification of insecticidal Xenorhabdus
strains.
The type strains and new isolates obtained by insect
entrapment were tested for toxicity when fed to insects. The type
strain X. nematophilus 9965 killed 100% of the insects
at a dose of 106 cells/cm2. When a total of 50 isolates obtained by entrapment from soil was screened for insecticidal
activity, two showed equivalent activity toward P. brassicae. This indicated that most of the strains obtained were
not as insecticidal to this insect under the conditions used. The three
active isolates were characterized by PCR-restriction fragment length
polymorphism (RFLP) analysis of their 16S rRNA gene and compared to the
type strains and a small selection of uncharacterized isolates. The 16S
rRNA RFLP patterns of the active strains were identical and included
the type strain of X. nematophilus 9965. Since more
than four enzymes were used to generate these patterns, the active
strains were therefore identified as subspecies of X. nematophilus (7, 10). One of these strains, PMFI296,
was studied in greater detail.
Cloning and expression of the insecticidal activity of
X. nematophilus PMFI296.
In a screen of
more than 500 E. coli clones containing cosmids with inserts
of X. nematophilus PMFI296 genomic DNA (ca. 40 kb), 2 were found to have insecticidal activity (Table
1). Both clones (cHRIM1 and cHRIM2) were
mapped with the enzymes BamHI, EcoRI,
HindIII, SacI, and SalI. Cosmid
cHRIM1 was found to have an insert of approximately 39 kb, while cosmid
cHRIM2 had a larger insert with an approximate size of 43 kb. The
restriction pattern of the clones indicated that the insert in cHRIM1
was a slightly smaller internal fragment of the insert in cHRIM2.
E. coli (cHRIM1) grown at 30°C had the greatest
insecticidal activity of these cosmids; however, the LC50
of these cells was ca. 1/50 of that obtained from the original strain
(Table 1). This loss in activity may be attributed to the presence on
cHRIM1 of only some of the toxins of strain PMFI296, the poor
expression of these genes in E. coli, or the degradation of
the toxins after expression. The protein profiles of X. nematophilus cells and E. coli clones are shown in
Fig. 1. One large protein of ca. 280 kDa
was present in X. nematophilus PMFI296 cells. Its size
(>250 kDa) and N'-terminal sequence (MIKVNELLDK) indicated
that this protein was XptA1, a toxin coded by the xptA1 gene
on cHRIM1 and shown here to be essential for insecticidal activity. In
X. nematophilus this protein is expressed at a
reasonable level and is clearly seen in the total cell protein profile
when the gel is stained with Coomassie blue. In E. coli
(cHRIM1) this protein cannot be detected using Coomassie blue staining.
This indicates that the XptA1 protein is present at a lower level in
the E. coli cells compared to X. nematophilus cells. When a more sensitive protein stain is used
(SYPRO), a protein of the correct size can be seen in E. coli (cHRIM1) cells. Insufficient protein was present to obtain
any protein sequence from this band; however, a protein of similar size
was not detected in E. coli cells (data not shown).
Therefore, the expression or stability of this protein would seem to
account for a significant proportion of the reduced insecticidal
activity of the E. coli cosmid clone.

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FIG. 1.
SDS-PAGE analysis of cell extracts from X. nematophilus pMFI296 and E. coli clones. (A) Lane 1, X. nematophilus pMFI296; lane 2, E. coli;
lane 3, E. coli (cHRIM1); and lane 4, E. coli
(338/2) stained with coomassie brilliant blue. (B) Lane 1, E. coli (cHRIM1) stained with SYPRO Orange. The position of XptA1 is
marked with an arrow. Size markers (M) are presented (in
kilodaltons).
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Sequence analysis of cHRIM1.
The complete sequence of cHRIM1
was obtained. The insert size is 38.4 kb and has an average G+C
composition of 34.6%, which is low but equivalent to other members of
the Enterobacteriaceae. Similarity searches have revealed
four complete and one incomplete predicted open reading frames that
illustrate differing levels of homology to insecticidal protein
toxins that have been identified in P. luminescens (9,
13). Figure 2 displays a map
of cHRIM1 indicating their position, and Table
2 summarizes the names given to these
genes and the homologies detected. The genes were designated xpt, for Xenorhabdus protein toxin, grouped A to
D, and further numbered according to the level of DNA homology and
overall size. Two similar genes were identified: xptA1 and
xptA2. Both of these genes and their predicted proteins
showed homology to each other and to the tcb and
tcd genes (40 to 45% identity) and the tcaB and
tccA genes (26 to 40% identity) present in P. luminescens. The arrangement of xptA1 and
xptA2 indicates that they are convergently transcribed.
Since they are homologous genes and close, this arrangement may prevent
homologous recombination and rearrangement of the DNA in this region.
The greatest similarity of the XptA1 and XptA2 proteins was to the Tcb
and Tcd proteins. A multiple sequence alignment of these proteins
indicates areas with different levels of similarity (Fig.
3). The last 700 amino acids of these
proteins (C'-terminal region) showed the greatest overall levels of
protein similarity (above their average similarity). Two other smaller regions before this area also showed higher levels of similarity. These regions with greater overall similarity may serve a similar function and may be unable to vary to the same extent as other areas of
the protein.

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FIG. 2.
Characterization of the contribution of genes on cHRIM1
to insecticidal activity. (A) Map indicating the effect of transposon
insertions in genes, including insertions that did not alter
insecticidal activity (active) and those that resulted in the loss of
insecticidal activity (inactive). Scos, cosmid vector. (B) Map of
the insert in the smallest active clone 338/2 constructed using the
SalI site at the end of the chitinase gene (chi)
and one transposon insertion obtained at the end of the
xptA2 gene (dotted lines). (C) Map of insert in plasmid
pHRIM801, where the xptA1 gene was expressed from the
bacteriophage PL promoter
(PL).
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TABLE 2.
Similarity of predicted proteins and regions of DNA on
cosmid cHRIM1 to sequences on the SWISSPROT and EMBL databases as
determined by using the program FASTA (6.0)a
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FIG. 3.
Multiple sequence comparison of the protein sequences
XptA1 and XptA2 from X. nematophilus and TcbA and TcdA
from P. luminescens using the package Plotsimilarity.
Scores at amino acid positions along the alignment are presented
(Henikoff-Henikoff amino acid similarity score, which ranges from 4
to +11), with the average similarity score represented by a dashed
line.
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Between the xptA1 and xptA2 genes, two further
predicted open reading frames are present, xptB1 and
xptC1, which show the greatest similarity to the
tccC (48% identity) and tcaC (49% identity) genes of P. luminescens, respectively (8, 13).
An additional gene that is not complete on the cosmid cHRIM1,
xptD1, was found to have similarity to the tccB,
tcbA, and tcaB genes (31 to 39% identity) in P. luminescens (8, 13). Therefore, on cHRIM1 four
complete genes and one incomplete gene with homology to others implicated in insecticidal activity have been identified. As Table 1
illustrates, these genes also show a degree of homology to one and
another between the different groups.
In addition to these toxin genes, a small region of DNA upstream of the
xptA1 gene encodes for a predicted protein (648 amino acids)
that shows similarity to chitinase protein sequences. The greatest
similarity to the exochitinase protein (EMBL accession no. 052863, 695 amino acids) from the Glossina morsitans S-endosymbiont was
detected (38% identity); this bacterium is also a member of the gamma
subdivision of the proteobacteria. The close proximity of the predicted
chitinase gene and the insecticidal toxin genes further indicates that
this is a cluster of pathogenicity factors on the chromosome of
PMFI296, all of which may be involved to some degree in the overall
insecticidal activity observed for this cosmid clone.
Other gene and predicted protein sequence homologies were also
identified on cHRIM1 that relate to DNA mobility; these are illustrated
in Fig. 4. An insertion sequence (IS) was
located 1,328 bp upstream of the xptA1 gene, which
transcribes toward the start of this gene. The IS is homologous to
IS630 detected in Salmonella species and other
Enterobacteriaceae (26). This insertion
sequence has an imperfect inverted repeat of the sequence ATTATGAAAACTTATTTAA and has a single 1,041-bp open reading
frame coding for a 347-amino-acid transposase (58% sequence identity to other transposases). This structure is typical of insertion sequences of this class (28). Just 814 bp upstream of the
insertion sequence is an open reading frame that shows similarity (47%
identity) to a putative transposase present on plasmid PMT-1 from
Yersinia pestis (25), and a direct repeat of
the sequence ATAAAATTTTCCGG on either side of this gene was
detected. Finally, a small area of DNA showed similarity (47%
identity) to the C'-terminal half of a bacteriophage P2 primase protein
(34). This area of similarity lies at the extreme edge of
the cosmid clone, and it is possible that other areas of a complete
phage genome lie upstream of this region. The presence of an IS
element, a putative transposase, and bacteriophage DNA sequences
adjacent to the toxin genes highlights the potential mobility of the
DNA within this region.

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FIG. 4.
Map of cHRIM1 indicating the position of mobile elements
and areas not related to known insecticidal genes. Restriction sites
for SalI and BamHI are shown. transp.,
hypothetical transposase, retro., retrotransposon; phage, bacteriophage
DNA; mit1 and mit2, AT-rich regions similar to mitochondrial DNA; Scos,
cosmid vector (size in kilobase pairs).
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Unusually, areas of the cHRIM1 sequence show considerable similarity
(up to 60% identity) to mitochondrial DNA sequences from nematodes and
other eukaryotic organisms (Fig. 4, mit1 and mit2). Upstream of the
xptA2 gene, before the phage primase region, the DNA shows
similarity (up to 60% identity) to mitochondrial rRNA, the
mitochondrial retrotransposase (R1), and AT-rich intergenic regions
with possible replication functions (mit1). For bacteria, the presence
of this unusual region of DNA further indicates greater DNA mobility
than expected. In addition, DNA homology to a tRNA gene (65% identity)
and regions of similarity to mitochondrial and eukaryotic DNA (55 to
65% identity) was detected in the regions surrounding the insertion
sequence and the putative bacterial transposase gene (mit2). The
separation of these two regions may indicate that the block of DNA from
the start of the xptA2 gene through to the start of the
xptA1 gene has integrated as one unit into this area. The
chitinase and truncated xptD1 gene, although linked to this
region by sharing homology to genes implicated with insecticidal
activity, may represent a separate unit.
Identification of the genes on cHRIM1 involved in insecticidal
activity.
To characterize the contribution of different genes and
DNA sequence(s) to the toxic activity of E. coli cells
containing cHRIM1, transposon mutagenesis of the insert was performed.
The PstI insert in pHRIM555, comprising the whole of the
insert in cHRIM1 and a small region of the original cosmid (Supercos1)
was mutated with the transposon Tn3. A total of 110 transposon mutants in pHRIM555 were generated. A total of 16 mutants
were mapped by digestion with HindIII and EcoRI,
and in all cases a different restriction pattern was obtained,
indicating that a diversity of insertion points were obtained. Of the
110 mutants, only 6 showed a loss of insecticidal activity. The
insertion points of the six nonactive strains were identified, and
these were located within the xptA1 gene. A number of other
transposon insertions were sequenced to determine their location.
Transposon insertions were found in the xptA2, xptD1, and
chi genes, and no loss in insecticidal activity toward
P. brassicae was detected (Fig. 2). These results indicated
that the expression of these genes did not contribute to the overall
insecticidal activity of E. coli (cHRIM1). Two deletions of
the cosmid were made. Using the SalI sites in the cosmid and
at the end of the predicted chitinase gene (chi), a deletion
of cHRIM1 removing the xptD1 and chi genes was
made. Also, using an AT2 transposon mutant (Tn116), with an insertion at the end of the xptA2 gene, a deletion of the
mit1 region and xptA2 gene was made. The resulting clone
(338/2) when expressed in E. coli was as insecticidal as
E. coli (cHIRM1). On this clone the xptA1, xptB1,
and xptC1 genes are complete (Fig. 2B). Transposon mutants
in the xptC1 and xptB1 genes were not obtained
with the Tn3 transposon, and their individual contributions to insecticidal activity could not be determined. It is possible that
an insertion in these genes resulted in DNA rearrangements or produced
a clone that was lethal to the host cell and was not represented in the
transposon library. Plasmid clones with smaller inserts than that
present in clone 338 were not insecticidal (data not shown).
Insecticidal activity of xptA1.
The
xptA1 gene that encodes for a protein with a predicted size
of 287 kDa and upstream from the ATG start (
8 bp) is a predicted ribosomal binding site (RBS; AGGA). To insert the
xptA1 gene under the control of the bacteriophage lambda
PL promoter, the cosmid cHRIM1 was cut with
NotI and the 14-kb fragment was inserted into the
NotI site of pLEX to create plasmid pHRIM800. Plasmid
pHRIM800 was cut with KpnI and AflII and
religated in the presence of the linker 5'-TTAAGTAC-3' (0.5 pmol/µl) to create plasmid pHRIM801. In this plasmid the RBS site and
ATG start of the xpt1A gene was brought close to the
PL promoter. When expression from the
PL promoter was induced in E. coli, a
large protein greater than 250 kDa was seen, which was not present in
E. coli cells (Fig. 5). The
N'-terminal sequence of this protein (10 amino acids) was determined
and was identical to the predicted xptA1 gene product. With
induction at 37°C for 18 h, most of this protein was found in
inclusion bodies and no insecticidal activity was detected. With
shorter periods of induction at 30°C, more of this protein was found
in the soluble fraction (Fig. 5). E. coli (pHRIM801) cells
were insecticidal (Table 1), reducing larval size and killing when
applied at a high concentration. The best results were obtained with
induction at 30°C for 18 h. At the levels used, the control E. coli cells did not kill P. brassicae larvae,
and therefore the LC50 value was greater than the detection
limit (Table 1). No difference between the insecticidal activity
of the soluble fraction and the inclusion body sample from E. coli (pHRIM801) was detected. The results indicated that the
overall insecticidal activity of the XptA1 protein was low.

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|
FIG. 5.
SDS-PAGE analysis of the expression of xptA1
from the PL promoter in E. coli
cells. Whole-cell extracts after 18 h of growth at 37°C. Lane 1, E. coli (pHRIM600); lane 2, E. coli. Cell
fractions after growth for 4 h at 30°C (lanes 3 and 5) and for
18 h at 30°C (lanes 4 and 6). Samples were separated into
inclusion bodies (lanes 3 and 4) and soluble fractions (lanes 5 and 6).
Markers (M) are presented (in kilodaltons).
|
|
 |
DISCUSSION |
A few bacterial isolates from insect parasitic nematodes when fed
to P. brassicae quickly stopped larval feeding and caused mortality within 24 h. The highly active isolates were all
identified as strains of X. nematophilus. From one of
these a region of DNA encoding proteins with insecticidal
activity toward P. brassicae was cloned. The smallest cosmid
clone (cHRIM1) was found to have a 39-kb insert, which initially
could not be reduced in size without the loss of insecticidal activity
when expressed in E. coli. The way the insects were killed
and the physical properties of the insecticidal activity expressed in
the clone (including its high molecular weight, its sensitivity to heat
treatment, and the degree of proteinase K resistance) were similar to
those found in the original Xenorhabdus strain
(22). A lower level of insecticidal activity was detected
in this E. coli clone compared to that obtained for the
original X. nematophilus PMFI296 strain. When the
growth temperature for E. coli cells was reduced to 30°C,
the insecticidal activity was improved. However, at best E. coli (cHRIM1) cells had approximately 1/50 of the activity of the
original strain (Table 1). By comparing the levels of one known
protein toxin (XptA1) in E. coli (cHRIM1) to that
detected in X. nematophilus PMFI296, at least part of
the reduced insecticidal activity of the clone could be attributed to
poor expression or stability of this protein in E. coli. By
taking into account the differences in the protein levels where at
least a fivefold drop in expression is evident (Fig. 1) and the
respective insecticidal activities of the cells (Table 1), it is
estimated that the specific activity of the cloned toxins is unlikely
to exceed a tenfold reduction compared to the wild-type strain.
However, additional toxins on the chromosome of X. nematophilus not present on the cosmid cHRIM1 could also
contribute to the total insecticidal activity of the original strain. A
transposon mutagenesis study on cHRIM1 identified one open reading
frame (xptA1) that was central to insecticidal activity.
This gene was similar in structure and had homology to two genes
(tcb and tcd) identified in P. luminescens (10). A second gene on cHRIM1
(xptA2) was a similar size and shared homology with
xptA1. This indicates that a close family of toxin genes,
similar in size and sequence, exist between Xenorhabdus and
Photorhabdus species. The two predicted proteins
(XptA1 and XptA2) also shared a degree of similarity to other
insecticidal toxins identified in P. luminescens, i.e., TcaB
and TccB (10). This also indicates that a degree of
similarity exists between the different toxin groups. Using DNA and
protein similarity, four other genes (xptB1, -C1,
and -D1 and chi) previously implicated with
insecticidal activity were identified on cHRIM1.
Transposon mutagenesis and subcloning were used to assess the
involvement of these genes in the expression of insecticidal activity
in E. coli (cHRIM1). Three of the genes (xptA2,
xptD1, and chi) did not contribute to the insecticidal
activity seen toward P. brassicae. The individual
contribution of the two genes, xptB1 and
xptC1, could not be determined since Tn3
transposons in these genes were not detected. Since the smallest
active clone (338/2) contains both these genes and the xptA1
gene and since the overall level of insecticidal activity of the toxin
XptA1 is poor, one or both of these genes (xptB1 and
-C1) are needed for full activity. The isolation of cosmid
clones expressing proteins with insecticidal activity has provided this
insight into the gene interactions for toxin activity. This region can
now be introduced into other bacteria to assess any changes in the
expression of activity, or to complement different toxins such as those
from B. thuringiensis.
P. luminescens toxin genes when expressed individually
in E. coli were not insecticidal
(9). In contrast, the xptA1 gene from
X. nematophilus was insecticidal. The high level of
expression of the xptA1 gene from the bacteriophage
PL promoter may be responsible for our ability
to detect insecticidal activity for this single toxin. In addition, a
greater sensitivity of our target insect may also have been partly
responsible for this. Certainly, the XptA1 protein is insecticidal, and
it is also central for the activity of E. coli
(cHRIM1) cells. However, the combination of the different toxins
on the cosmid is important for overall activity. The cosmid
genomic cloning strategy adopted here may provide a useful
way for obtaining active proteins that are insecticidal when expressed
in heterologous hosts. This may provide a faster solution to the
expression of active toxins than studying purified toxins. For example,
if one or more of the gene products on cHRIM1 interacts with XptA1 to
activate it then, unless the activation step becomes obvious during the
purification of the active protein, it may become difficult to
determine the changes that have taken place in this protein. The
activated protein may have an altered structure, processed at either
end, or it may become protected in some way from inactivation in the
insect gut. These processes may be difficult to detect in a purified
peptide. Thus, in an E. coli strain expressing proteins from
a cosmid clone that has insecticidal activity, at least some of these
factors would have to be present on the clone. These interactions can
then be studied at the genetic level. However, strain PMFI296 may be
unusual and the key toxin genes may not be close together on the
chromosome in other strains, and thus a cloning approach would fail.
Different protein interactions may also be responsible for differences
in insecticidal activity seen toward other insect species. As such, the
xptA2 and chitinase genes may be important for full activity toward insects other than P. brassicae.
The fact that genes similar to those identified here in
X. nematophilus have been found in distantly
related strains of P. luminescens indicates that a
common set of insect toxins exist in bacteria associated with IPNs.
This suggests that either of these strains have had these genes since
they diverged from a common ancestor in which they may have been
required to fulfill a similar function or, alternatively, that gene
exchange has taken place either between these strains or between these
strains and a common, as-yet-unidentified strain in more recent times.
The presence of an insertion sequence, phage DNA, and mitochondrial DNA
near the toxin genes on cHRIM1 indicates that gene exchange between
strains is likely to have been involved in the distribution of toxin
genes. However, it is possible that this area on the chromosome may act
as a hot spot for the insertion of DNA coming from other sources. A
better understanding of these processes may be gained from the analysis
of a greater diversity of strains. The dependence of this bacteria on a
nematode host and its growth within an insect may explain how this
strain has acquired DNA that is similar to eukaryotic mitochondrial DNA
sequences through lateral DNA transfer in this close relationship. It
is interesting that the presence of homology to a tRNA gene and the
prediction of three tRNA genes near to the potential point of insertion
of the toxin genes shows similarity with the other mobile virulence regions in E. coli, Salmonella species,
Dichelobacter nodosus, and other bacteria
(5, 6, 19). In these instances, large segments of DNA also
insert into tRNA loci, and a number of independent insertion events may
have led to the mosaic structure now seen in the genomes of these
strains. As well as the presence of virulence determinants, the
presence of IS elements, tRNA genes, and phage genes are all
hallmarks of a pathogenicity island (19). We
therefore conclude that that the insert in cHRIM1 represents a
pathogenicity island on the genome of X. nematophilus PMFI296.
 |
ACKNOWLEDGMENTS |
This work was funded by the Ministry of Agriculture Fisheries and
Food (United Kingdom) and the Biological and Biotechnological Sciences
Research Council (United Kingdom).
We thank Umesh Patel at Cambridge Biosciences and Ruth Finch at
Horticulture Research International for their help in the DNA
sequencing work. We also thank Pat Barker at the protein sequencing unit, Babraham Institute (United Kingdom), for help with this work.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department
of Plant Pathology and Microbiology, Horticulture Research
International, Wellesbourne, Warwick CV35 9EF, United Kingdom. Phone:
01789-470382. Fax: 01789-470552. E-mail:
alun.morgan{at}hri.ac.uk.
 |
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Applied and Environmental Microbiology, May 2001, p. 2062-2069, Vol. 67, No. 5
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.5.2062-2069.2001
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