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J Bacteriol, April 1998, p. 1939-1943, Vol. 180, No. 7
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
Functions Encoded by Pyrrolnitrin Biosynthetic
Genes from Pseudomonas fluorescens
Sabine
Kirner,1
Philip E.
Hammer,2
D. Steven
Hill,2
Annett
Altmann,3
Ilona
Fischer,3
Laura J.
Weislo,4
Mike
Lanahan,4
Karl-Heinz
van Pée,3 and
James M.
Ligon2,*
Novartis Crop Protection,
Inc.,2 and
Novartis Seeds,
Inc.,4 Research Triangle Park, North
Carolina 27709, and
Institut für Mikrobiologie,
Universität Hohenheim, D-70593
Stuttgart,1 and
Institut für
Biochemie, TU Dresden, D-01062 Dresden,3
Germany
Received 11 August 1997/Accepted 13 January 1998
 |
ABSTRACT |
Pyrrolnitrin is a secondary metabolite derived from tryptophan and
has strong antifungal activity. Recently we described four genes,
prnABCD, from Pseudomonas fluorescens that
encode the biosynthesis of pyrrolnitrin. In the work presented here, we
describe the function of each prn gene product. The four
genes encode proteins identical in size and serology to proteins
present in wild-type Pseudomonas fluorescens, but absent
from a mutant from which the entire prn gene
region had been deleted. The prnA gene product catalyzes the chlorination of L-tryptophan to form
7-chloro-L-tryptophan. The prnB gene product
catalyzes a ring rearrangement and decarboxylation to
convert 7-chloro-L-tryptophan to
monodechloroaminopyrrolnitrin. The prnC gene product
chlorinates monodechloroaminopyrrolnitrin at the 3 position to form
aminopyrrolnitrin. The prnD gene product catalyzes
the oxidation of the amino group of aminopyrrolnitrin to a nitro group
to form pyrrolnitrin. The organization of the prn genes in
the operon is identical to the order of the reactions in the
biosynthetic pathway.
 |
TEXT |
The antibiotic pyrrolnitrin
[3-chloro-4-(2'-nitro-3'-chlorophenyl)pyrrole] (PRN) is
produced by many pseudomonads and has broad-spectrum antifungal
activity (1, 5, 12-14, 17). PRN has been implicated as an
important mechanism of biological control of fungal plant pathogens by
several Pseudomonas strains (12-14), including
P. fluorescens BL915, from which the prn
genes were isolated (10).
Tryptophan was identified as the precursor for PRN, based on the
feeding of cultures with isotopically labeled and substituted tryptophan (2, 7, 8, 17, 25). Biosynthetic pathways were
proposed as early as 1967 (7) and have been refined on the
basis of tracer studies and the isolation of intermediates (Fig.
1) (2, 8, 17, 19, 23, 25).
Recently, Hammer et al. (9) described the cloning and
characterization of a 5.8-kb DNA region which encodes the PRN
biosynthetic pathway. This DNA region confers the ability to produce
PRN when expressed heterologously in Escherichia coli and
contains four genes, prnABCD, each of which is required for
PRN production. In the research described here, we used mutants in
which each of the four genes was disrupted and strains which
overexpress the individual genes to elucidate the function of
each gene product in PRN biosynthesis.

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FIG. 1.
Biosynthetic pathways for PRN as proposed by van
Pée et al. (23) (A) and by Chang et al. (2)
(B). The reactions catalyzed by the PRN biosynthetic enzymes encoded by
the prnABCD genes are indicated above the appropriate
reaction arrows.
|
|
Bacterial strains and plasmids.
The bacterial strains and
plasmids used in this study are described in Table
1. Pseudomonas strains were
cultured in Luria-Bertani medium at 28°C. Antibiotics, when used,
were added at the following concentrations: tetracycline, 30 µg/ml;
and kanamycin, 50 µg/ml. The expression vector pPEH14 consists of the
Ptac promoter and rrnB ribosomal
terminator from pKK223-3 (Pharmacia, Uppsala, Sweden) cloned into the
BglII site of the broad-host-range plasmid pRK290
(4). Ptac is a strong constitutive
promoter in Pseudomonas (unpublished data). The PRN
biosynthetic genes are the coding regions described by Hammer et al.
(9). Each coding region was cloned from the translation
initiation codon to the stop codon by PCR with restriction sites added
to the ends to facilitate cloning. For prnB, the native GTG
initiation codon was changed to ATG. The clones were sequenced after
PCR.
Chemical standards.
7-Cl-D,L-tryptophan (7-CT) was synthesized
as described by van Pée et al. (24).
Monodechloroaminopyrrolnitrin (MDA) was extracted from
cultures of P. aureofaciens and verified as
described by van Pée et al. (23).
Aminopyrrolnitrin (APRN) was prepared from PRN by reduction with sodium
dithionite (22). PRN was synthesized according to the method
of Gosteli (6).
Western analysis.
To produce antigen, each prn gene
was subcloned into a pET3 vector and transformed into E. coli BL21(De3) (Novagen, Inc., Madison, Wis.). Inclusion
bodies were purified from induced cultures with protocols from Novagen.
Inclusion body protein (100 µg) was run on a preparative Laemmli
polyacrylamide electrophoresis gel, blotted to nitrocellulose filters,
and stained with Ponceau S. The major band was excised, solubilized in
dimethyl sulfoxide, and used by Duncroft, Inc. (Lovettsville, Va.), to
immunize goats and produce antiserum against each PRN protein.
Cultures of
P. fluorescens BL915 were grown for 48 h in Luria-Bertani medium with the appropriate antibiotics. The cells
were
pelleted and resuspended in a small volume of Tris-EDTA.
Sodium
dodecyl sulfate-polyacrylamide gel electrophoresis and
Western
analysis were performed as described by Sambrook et al.
(
21).
The primary antiserum (goat anti-PRN protein)
was diluted 1/1,000,
and the secondary antibody (rabbit anti-goat
immunoglobulin G
conjugated to peroxidase; Pierce, Rockford,
Ill.) was diluted
1/3,000. Bands were visualized with an enhanced
chemiluminescence
kit (Amersham, Arlington Heights, Ill.). This
Western analysis
demonstrated that each antibody recognized a
single protein band
from wild-type BL915, and these bands were not
present in BL915

ORF1-4
(Fig.
2). The molecular weights of the
recognized proteins were
consistent with the sizes predicted from the
gene sequences. Each
prn gene was expressed on a plasmid in
BL915

ORF1-4. In each case,
the protein product of the cloned gene
reacted only with the expected
antibody and was identical in size to
the band detected by that
antibody in wild-type BL915 (Fig.
2).

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FIG. 2.
Western blot analysis of the protein products of
prn genes cloned from P. fluorescens BL915.
Individual genes were expressed on plasmids in the host strain
BL915 ORF1-4. BL915 wild-type and BL915 ORF1-4 controls are
included on each blot. Blots A, B, C, and D were probed with antibodies
raised against the products of prnA, prnB,
prnC, and prnD, respectively. Arrows indicate the
positions of the 60- and 42-kDa molecular mass markers.
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|
Intermediate analysis and feeding experiments.
To determine
which biosynthetic intermediates were produced by the prn
gene deletion mutants, 2-day-old cultures were extracted with an equal
volume of ethyl acetate. The organic phase was dried under vacuum, and
the residue was dissolved in a small volume of methanol. Thin-layer
chromatography (TLC) was performed on silica-coated plates with toluene
or hexane-ethyl acetate (2:1) as the mobile phase. PRN, APRN, MDA, and
aminophenylpyrrole (APP) were visualized with van Urk's reagent as
described previously (22).
To further clarify which biosynthetic step was blocked in each deletion
mutant, intermediate feeding experiments were conducted.
Cultures (10 ml) were incubated at 28°C for 48 h. Biosynthetic
intermediates
were dissolved in a small volume of methanol and
added to 4 ml of
culture at the following final concentrations:
7-CT, 2.5 µg/ml; MDA,
25 µg/ml; APRN, 12.5 µg/ml. The cultures
were incubated for an
additional 4 h at 28°C and then extracted
with ethyl acetate and
analyzed by TLC and liquid chromatography-mass
spectrometry as
described above.
MDA, APRN, and PRN were not detected in cultures of BL915

ORF1 (Fig.
3), indicating that this mutant is
blocked at an early
step in PRN biosynthesis. BL915

ORF1 was able to
produce PRN when
7-CT, MDA, or APRN was supplied exogenously (Table
2). When
prnA was expressed in
the absence of other
prn genes (i.e., in BL915

ORF1-4),
7-chloro-
L-tryptophan (7-CLT) accumulated. The identity of
7-CLT
was verified by comparison of results of high-performance liquid
chromatography and mass spectra with chemically synthesized 7-CT.
These
results indicate that the
prnA gene product catalyzes the
chlorination of
L-tryptophan.

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FIG. 3.
Accumulation of PRN biosynthetic intermediates in
P. fluorescens BL915 and prn gene deletion
mutants derived from it. Extracts from 2-day-old cultures were
separated by TLC on silica plates with hexane-ethyl acetate (2:1
[vol/vol]) as the mobile phase. Metabolites were visualized with van
Urk's reagent. Arrows indicate the positions of MDA (olive green),
APRN (reddish brown), and PRN (purple).
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|
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TABLE 2.
Production of PRN by deletion mutants when supplied with
biosynthetic intermediates in the growth medium
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|
Hohaus et al. (
11) presented additional evidence of the
chlorinating activity of the
prnA gene product,
specifically, the
chlorination of
L-tryptophan to form
7-CLT by cell extracts from
P. fluorescens strains
which expressed the
prnA gene, but which
did not contain any
of the other
prn genes. To clarify which isomer
was
produced, Hohaus et al. (
11) extracted 7-CLT from the
bacteria
and oxidized it to the corresponding indole-3-pyruvic acid
with
amino acid oxidases. Since the isolated 7-CLT was degraded by
L-amino acid oxidase, but not by
D-amino acid
oxidase (
11),
it must be in the
L configuration.
The deduced amino acid sequence
for
prnA contains a
consensus NAD binding site (
9), and, indeed,
NADH is a
required cofactor for the
prnA gene product.
Cultures of BL915

ORF2 produced 7-CLT, but
7-chloro-
D-tryptophan (
11) and other PRN
biosynthetic intermediates were not
detected (Fig.
3). BL915

ORF2
produced PRN when supplied with
exogenous MDA or APRN, but not when
supplied with 7-CT (Table
2). When
prnB was expressed in
strain BL915

ORF1-4, exogenously
supplied 7-CT was converted to MDA
(Fig.
4). These results indicate
that the
prnB gene product catalyzes the rearrangement of the
indole
ring to a phenylpyrrole and the decarboxylation of 7-CLT
to convert
7-CLT to MDA. While it is somewhat surprising that
a single enzyme
carries out both the ring rearrangement and decarboxylation,
Chang et
al. (
2) postulated a mechanism for such a reaction
on a
single enzyme some 16 years ago. The
prnB gene product also
catalyzed the production of APP (Fig.
4), presumably by using
tryptophan as a substrate.

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FIG. 4.
In vivo conversion of PRN biosynthetic intermediates by
the products of single prn genes. Individual genes were
expressed on plasmids in the host strain BL915 ORF1-4, and
biosynthetic intermediates were added to the culture medium as
indicated. Culture extracts were separated by TLC on silica plates with
toluene as the mobile phase. Metabolites were visualized with van
Urk's reagent. Arrows indicate the positions of APP (dark green), MDA
(olive green), APRN (reddish brown), and PRN (purple).
|
|
MDA accumulated in cultures of BL915

ORF3, but APP, APRN, and PRN
were not detected (Fig.
3). BL915

ORF3 was able to produce
PRN when
supplied with APRN in the culture medium, but not when
supplied with
7-CT or MDA (Table
2). Strain BL915

ORF1-4 expressing
prnC converted exogenously supplied MDA to APRN (Fig.
4).
These
data indicate that the
prnC gene product catalyzes the
chlorination
of MDA to form APRN. Cell extracts of the
P. fluorescens strain
which overexpresses the
prnC gene
(but does not contain the other
prn genes) can also catalyze
the chlorination of MDA to form APRN
(
11).
The
prnC gene is homologous to the
chl gene from
Streptomyces aureofaciens, which encodes a chlorinating
enzyme for tetracycline
biosynthesis (
3,
9). Like
prnA, the
prnC deduced amino acid
sequence
contains a consensus NAD binding region (
9), and NADH
is
required for the chlorination of MDA (
11). While both
prnA and
prnC encode halogenating enzymes, they
show no homology to
previously cloned haloperoxidases (
9) or
to each other. Furthermore,
in contrast to haloperoxidases
(
16), the two NADH-dependent
halogenating enzymes in the PRN
biosynthesis pathway are substrate
specific (i.e., the tryptophan
halogenase does not catalyze the
chlorination of MDA and vice versa)
(
11).
APRN accumulated in cultures of BL915

ORF4 (Fig.
3), and this mutant
was not able to produce PRN when supplied with any of
the known PRN
biosynthetic intermediates. Strain BL915

ORF1-4
expressing
prnD converted exogenously supplied APRN to PRN (Fig.
4).
These results indicate that the
prnD gene product catalyzes
the oxidation of the amino group of APRN to a nitro group forming
PRN.
In vitro experiments by Kirner and van Pée (
15) had
suggested
that this reaction is catalyzed by a chloroperoxidase;
however,
gene disruption experiments demonstrated that
chloroperoxidases
are not involved in PRN biosynthesis in vivo
(
16). Instead,
this oxidation is more likely to be catalyzed
by a class IA oxygenase
(
20), as suggested by the homology
of
prnD with these enzymes
(
9).
We have shown that each
prn gene encodes a protein found in
the wild-type BL915 strain and have demonstrated in vivo that
these
four gene products carry out four biochemical steps which
convert
L-tryptophan to PRN. None of the conversions were observed
in strain BL915

ORF1-4, from which the entire 5.8-kb
prn
gene
region has been deleted (Fig.
4). The arrangement of the
genes
in the operon is identical to the sequence of reactions in the
biosynthetic pathway proposed by van Pée et al. (
23)
(Fig.
1).
Chang et al. (
2) proposed an alternate biosynthetic scheme
(Fig.
1B) and reported the conversion of exogenously supplied
APP to
PRN in vivo. Similarly, Zhou et al. (
25) reported the
conversion of APP to APRN in a cell-free system. These workers
concluded that APP is an intermediate in PRN biosynthesis and
that ring
rearrangement precedes chlorination (Fig.
1B). In the
present study,
APP accumulated only in strains which overexpressed
the
prnB
gene. Furthermore, APP was not detected in cultures of
BL915

ORF1,
which contains functional
prnBCD genes expressed from
the
native promoter, as would be expected if the ring rearrangement
(catalyzed by the
prnB gene product) occurs before the first
chlorination
step (catalyzed by the
prnA gene product). Like
Hamill et al.
(
8) and van Pée et al. (
23),
we demonstrated that exogenously
supplied 7-CT is converted to PRN.
These results, together with
the finding that the gene product of
prnA catalyzes the NADH-dependent
chlorination of
L-tryptophan to 7-CLT (
11), support the
biosynthetic
pathway proposed by van Pée et al. (
23)
(Fig.
1A) and suggest
that APP is a side product or dead-end
metabolite. Purification
and kinetic characterization of the
prnA and
prnB gene products,
including
investigations of substrate specificity and regioselectivity,
will
further clarify the roles of 7-CLT and APP in the PRN biosynthetic
pathway.
If APP is indeed a dead-end metabolite, it would be advantageous to
tightly regulate the amount of
prnB gene product present
in
cells, thus minimizing the diversion of substrate into APP.
The
prnB gene begins with GTG (
9), which is a two- to
threefold-less-efficient
initiation codon than ATG (
18);
however, the
prnB open reading
frame is apparently
translationally coupled to the
prnA open reading
frame
(
9). Coupling increases translational efficiency and
is
thought to be a mechanism to ensure coordinate expression of
the
coupled genes (
18). In PRN biosynthesis, translational
coupling
of
prnA and
prnB may be a mechanism to
regulate the level of
prnB gene product present in cells and
minimize the diversion of tryptophan
to APP.
 |
ACKNOWLEDGMENTS |
This work was supported by Novartis Crop Protection, Inc., the
Deutsche Forschungsgemeinschaft, the Sächsische Staatsministerium für Umwelt und Landesentwicklung, and the Fonds der Chemischen Industrie.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Novartis Crop
Protection, Inc., 3054 Cornwallis Rd., Research Triangle Park, NC
27709. Phone: (919) 541-8645. Fax: (919) 541-8557. E-mail:
james.ligon{at}cp.novartis.com.
 |
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J Bacteriol, April 1998, p. 1939-1943, Vol. 180, No. 7
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
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