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Journal of Bacteriology, April 2000, p. 2191-2199, Vol. 182, No. 8
Department of Biochemistry, Groningen
Biomolecular Sciences and Biotechnology Institute, University of
Groningen, 9747 AG Groningen, The Netherlands,1
and The Questor Centre, The Queen's University of Belfast,
Belfast BT9 5AG, United Kingdom2
Received 10 November 1999/Accepted 27 January 2000
The haloalkane-degrading bacteria Rhodococcus
rhodochrous NCIMB13064, Pseudomonas pavonaceae 170, and Mycobacterium sp. strain GP1 share a highly conserved
haloalkane dehalogenase gene (dhaA). Here, we describe the
extent of the conserved dhaA segments in these three
phylogenetically distinct bacteria and an analysis of their flanking
sequences. The dhaA gene of the 1-chlorobutane-degrading strain NCIMB13064 was found to reside within a 1-chlorobutane catabolic
gene cluster, which also encodes a putative invertase (invA), a regulatory protein (dhaR), an alcohol
dehydrogenase (adhA), and an aldehyde dehydrogenase
(aldA). The latter two enzymes may catalyze the oxidative
conversion of n-butanol, the hydrolytic product of
1-chlorobutane, to n-butyric acid, a growth substrate for
many bacteria. The activity of the dhaR gene product was
analyzed in Pseudomonas sp. strain GJ1, in which it
appeared to function as a repressor of dhaA expression. The
1,2-dibromoethane-degrading strain GP1 contained a conserved DNA
segment of 2.7 kb, which included dhaR, dhaA,
and part of invA. A 12-nucleotide deletion in
dhaR led to constitutive expression of dhaA in
strain GP1, in contrast to the inducible expression of dhaA
in strain NCIMB13064. The 1,3-dichloropropene-degrading strain 170 possessed a conserved DNA segment of 1.3 kb harboring little more than
the coding region of the dhaA gene. In strains 170 and GP1,
a putative integrase gene was found next to the conserved
dhaA segment, which suggests that integration events were
responsible for the acquisition of these DNA segments. The data
indicate that horizontal gene transfer and integrase-dependent gene
acquisition were the key mechanisms for the evolution of catabolic
pathways for the man-made chemicals 1,3-dichloropropene and
1,2-dibromoethane.
Synthetic haloalkanes form an
important class of environmental pollutants because of their widespread
use in industry and agriculture, persistence in the environment, and
potential carcinogenicity. The poor biodegradability of these chemicals
is mainly due to the inability of microorganisms to effectively
metabolize these unnatural compounds. Nevertheless, microbial
communities exposed to synthetic haloalkanes often respond by
expressing specific pathways that degrade these molecules in order to
exploit them as growth substrates. Since synthetic haloalkanes are
xenobiotic compounds of recent origin, the way in which genes have been
assembled to form functional catabolic pathways is an interesting
subject for studying microbial evolution and gene transfer.
Rhodococcus rhodochrous NCIMB13064, isolated in the United
Kingdom from a soil sample obtained from an industrial site which had
previously been exposed to chlorinated alkanes, is capable of utilizing
1-chlorobutane and several other haloalkanes as the sole carbon and
energy source (9). The cleavage of the carbon-halogen bond
in 1-chlorobutane, which is the key step in its catabolism, is
catalyzed by an inducible hydrolytic haloalkane dehalogenase (DhaA) and
results in the formation of n-butanol. This intermediate is
subsequently oxidized in two steps to n-butyric acid (Fig. 1), which can serve as a growth substrate
for many bacteria. The haloalkane dehalogenase gene (dhaA)
was shown to be located on the autotransmissible plasmid pRTL1
(22) and was cloned and sequenced (23).
0021-9193/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Roles of Horizontal Gene Transfer and Gene
Integration in Evolution of 1,3-Dichloropropene- and
1,2-Dibromoethane-Degradative Pathways
ABSTRACT
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Abstract
Introduction
Materials and Methods
Results and Discussion
References
INTRODUCTION
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Abstract
Introduction
Materials and Methods
Results and Discussion
References
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FIG. 1.
Catabolic pathways for haloaliphatics. (A)
1-Chlorobutane in R. rhodochrous NCIMB13064. (B)
1,3-Dichloropropene in P. pavonaceae 170. (C)
1,2-Dibromoethane in Mycobacterium sp. strain GP1.
Abbreviations: DhaA and DhaAf, haloalkane dehalogenases;
H-lyase, halohydrin halogen-halide lyase; CaaD, 3-chloroacrylic acid
dehalogenase; X, alcohol dehydrogenase cofactor; Y, aldehyde
dehydrogenase cofactor.
The gram-negative 1,3-dichloropropene-utilizing bacterium Pseudomonas pavonaceae 170, isolated in The Netherlands from soil that was repeatedly treated with the nematocidic soil fumigant 1,3-dichloropropene, was shown by PCR amplification to possess a haloalkane dehalogenase gene identical to the dhaA gene of the gram-positive strain NCIMB13064 (35). In contrast to the inducible production of DhaA in strain NCIMB13064, DhaA is constitutively produced in strain 170 and catalyzes the first step in the degradation of 1,3-dichloropropene (Fig. 1).
Recently, we demonstrated that the 1,2-dibromoethane-degrading organism Mycobacterium sp. strain GP1, which was isolated by prolonged batch enrichment from a mixed bacterial culture, also contains a haloalkane dehalogenase gene (dhaAf) that is very similar to the dhaA gene found in strain NCIMB13064 (36). The haloalkane dehalogenase encoded by dhaAf is identical to DhaA, except for three amino acid substitutions and a 14-amino-acid extension at the C terminus. Nucleotide sequence analysis indicated that the dhaAf gene was formed by a fusion of a dhaA gene with the last 42 nucleotides of a hheB gene, which encodes a haloalcohol dehalogenase (50). The haloalkane dehalogenase (DhaAf) is constitutively produced in strain GP1 and catalyzes the conversion of 1,2-dibromoethane to 2-bromoethanol, which is further metabolized via ethylene oxide (Fig. 1).
The presence of a highly conserved dhaA gene in the three phylogenetically different organisms R. rhodochrous NCIMB13064, P. pavonaceae 170, and Mycobacterium sp. strain GP1 suggests that dhaA has been distributed among these organisms by horizontal transfer. To determine the size of the transferred DNA fragments and to identify the mechanisms that were involved in the distribution process, we have analyzed the DNA regions flanking the dhaA gene in these three haloalkane-utilizing strains. The results suggest that the haloalkane dehalogenase gene regions of strains 170 and GP1 originate from a 1-chlorobutane catabolic gene cluster similar to the one that is present on plasmid pRTL1 in strain NCIMB13064. Horizontal gene transfer and integrase-dependent acquisition of existing DNA fragments harboring the dhaA gene were probably the key steps during the evolution of 1,3-dichloropropene- and 1,2-dibromoethane-degradative pathways. Furthermore, the constitutive expression of dhaA in strains 170 and GP1, in contrast to the inducible expression of dhaA in strain NCIMB13064, is explained by the absence or inactivation of the regulatory gene dhaR.
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MATERIALS AND METHODS |
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Abstract
Introduction
Materials and Methods
Results and Discussion
References
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Materials. Restriction enzymes, Taq DNA polymerase, T4 DNA ligase, the DNA-packaging kit, and materials used for Southern blot hybridization were purchased from Boehringer Mannheim (Mannheim, Germany). 1,2-Dibromoethane was supplied by Acros Organics (Geel, Belgium). The oligonucleotides used as primers were supplied by Eurosequence BV (Groningen, The Netherlands).
Bacterial strains, plasmids, and growth conditions.
The
characteristics of the 1,3-dichloropropene-degrading bacterium P. pavonaceae 170, formerly known as Pseudomonas cichorii 170 (44), and of the 1,2-dibromoethane-degrading organism
Mycobacterium sp. strain GP1 are given elsewhere (35,
36). R. rhodochrous NCIMB13064 contains the large
catabolic plasmid pRTL1 (22) and is able to use
1-chlorobutane as the sole carbon and energy source (9).
Escherichia coli strains HB101 (7) and JM101
(49) and plasmid pBluescript SK(
) (Stratagene, Leusden,
The Netherlands) were used for routine cloning experiments. E. coli HB101(pRK600) (13) was the helper strain used for
mobilizing pLAFR3/5- and pDSK519-derived plasmids in triparental
matings with the recipient Pseudomonas sp. strain GJ1
(17). Plasmid pDSK519 and cosmids pLAFR3 and pLAFR5 are
mobilizable broad-host-range vectors (19, 39). Recombinant
cosmid pLTL1k contains the 1-chlorobutane catabolic gene cluster of
strain NCIMB13064 (23) and was used as template for DNA
sequencing and as the source for some cloning and expression experiments described here. Recombinant cosmids pGP1-4B5, which contains the dhaAf gene region of strain GP1
(36), and pPC33, which contains the dhaA gene
region of strain 170 (this study), were used as templates for DNA sequencing.
-D-galactopyranoside (X-Gal;
40 µg/ml) and isopropyl--D-thiogalactopyranoside
(IPTG; 0.4 mM).
DNA techniques. General procedures for cloning, transformation, and DNA manipulation were performed essentially as described by Sambrook et al. (38). Triparental matings were carried out as described by Janssen et al. (18). Isolation of total genomic DNA from strains NCIMB13064, 170, and GP1 was performed according to the phenol extraction procedure described previously (35). The IS2112- and IS1071-specific probes used in hybridization experiments were obtained by PCR amplification by using primers and conditions as previously described (21, 48). DNA fragments were purified by using the Qiaquick PCR purification kit (Qiagen). Southern blot hybridization experiments were performed as described previously (21).
Crude extracts and dehalogenase assays. Pseudomonas and E. coli cells were harvested in the late-exponential growth phase by centrifugation (10 min at 10,000 × g), were washed with 1 volume of 50 mM Tris-sulfate buffer (pH 8.2), and were disrupted at 4°C in an appropriate amount of this buffer by sonication (10 s per ml of suspension at a 70 W output in a Vibra cell sonicator). A crude extract was obtained by centrifugation (45 min at 16,000 × g).
Haloalkane dehalogenase activities were measured by incubating an appropriate amount of cell extract with 3 ml of 5 mM 1,2-dibromoethane in 50 mM Tris-sulfate buffer (pH 8.2) at 30°C. Halide liberation was monitored colorimetrically as described previously (20). All dehalogenase activities are expressed as units per miligram; 1 U was defined as the amount of enzyme that catalyzes the production of 1 µmol of halide per min. Protein concentrations were estimated with Coomassie brillant blue by using bovine serum albumin as the standard. Enzyme assays were carried out twice, and the differences in specific activities were less than 10%.Cloning of the dhaA gene region from P. pavonaceae 170.
A genomic library of P. pavonaceae 170 was constructed by using cosmid vector pLAFR3
according to a previously described procedure (39).
Individual cosmid clones were screened for dehalogenase activity by
monitoring halide production upon incubation with 1,2-dibromoethane.
Out of 5,000 E. coli HB101 clones tested, two dehalogenase-positive clones were found. Recombinant cosmids pPC8 and
pPC33 encoding haloalkane dehalogenase were isolated from these two
HB101 clones and were digested with BamHI. Both cosmids had
a 3-kb BamHI fragment in common. The 3-kb BamHI
fragment of pPC33 was ligated into the BamHI site of
pBluescript SK(). The ligation mixture was used to transform cells of
E. coli JM101, and transformants were plated on LBZ plates
containing ampicillin, X-Gal, and IPTG. Ampicillin-resistant white
colonies displaying haloalkane dehalogenase activity with
1,2-dibromoethane were selected. Plasmid DNA (pSK45) of one of these
colonies was isolated and used as template for DNA sequencing. The
nucleotide sequences of DNA regions flanking the 3-kb BamHI
fragment were determined by using cosmid pPC33 directly as a template
for DNA sequencing.
Nucleotide sequencing and analysis. DNA sequencing was performed as previously described (21, 36). The nucleotide sequence data were analyzed by using the programs supplied in the DNASTAR software package (DNASTAR Inc., Madison, Wis.) or those supplied in the PC/GENE software package (Genofit, Geneva, Switzerland). Searches for nucleotide and amino acid sequence similarities were carried out by using the BLAST program (3) and the DDBJ, EMBL, and GenBank databases. Protein sequences were aligned by using CLUSTAL W (41), and alignments of nucleotide sequences were made by using LALIGN (Institut de Génétique Humaine, Montpellier, France).
Nucleotide sequence accession numbers. The nucleotide sequence data of the haloalkane dehalogenase gene regions from R. rhodochrous NCIMB13064, P. pavonaceae 170, and Mycobacterium sp. strain GP1 have been submitted to the DDBJ, EMBL, and GenBank databases under accession no. L49435, AJ250371, and AJ250372, respectively.
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RESULTS AND DISCUSSION |
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Abstract
Introduction
Materials and Methods
Results and Discussion
References
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Sequence analysis of the dhaA gene region from R. rhodochrous NCIMB13064.
The dhaA gene of the
1-chlorobutane-degrading bacterium R. rhodochrous NCIMB13064
is located on the 100-kb plasmid pRTL1 (23). A 13.1-kb DNA
fragment of pRTL1, including a 8.2-kb region upstream and a 4-kb region
downstream of dhaA, was sequenced (Fig.
2). The dhaA gene sequence and
the analysis of insertion element IS2112, which is located
approximately 6 kb upstream of dhaA (Fig. 2), were described
previously (21, 23).
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The extent of the conserved dhaA gene fragments in P. pavonaceae 170 and Mycobacterium sp. strain GP1. When the haloalkane dehalogenase gene regions of P. pavonaceae 170 and R. rhodochrous NCIMB13064 are compared, the conserved DNA fragment in strain 170 can be seen to include a region of about 1.3 kb that harbors little more than the coding region of the dhaA gene (Fig. 2). The dhaA genes of strains 170 and NCIMB13064 are completely identical. The first 37 nucleotides upstream of the start codon of dhaA are also identical in both strains, after which there is a deletion of 98 nucleotides in the Pseudomonas sequence when compared to the Rhodococcus sequence (Fig. 2 and 3). Upstream of this deletion, the sequences continue to be identical for 268 nucleotides and then abruptly become completely unrelated. The 98-nucleotide deletion in the Pseudomonas sequence includes exactly the DNA sequence between the 13-bp directed repeat as well as one of the repeated sequences itself (Fig. 3). The formation of this deletion may be explained by DNA strand slippage, which allows one repeated sequence to mispair with the complement of the other (2).
The two sequences are identical for only 77 nucleotides downstream of the dhaA gene. The following 60 nucleotides in the Pseudomonas sequence (nucleotides 3600 to 3659) are identical to a fragment downstream of aldA (nucleotides 12313 to 12372) in the Rhodococcus sequence (Fig. 3). This suggests that a large deletion of about 3.2 kb, including the alcohol and aldehyde dehydrogenase genes, has occured in the Pseudomonas sequence when compared to the Rhodococcus sequence (Fig. 2). No similarity between the two sequences was found further downstream. When the haloalkane dehalogenase gene regions of Mycobacterium sp. strain GP1 and R. rhodochrous NCIMB13064 are compared, the conserved DNA fragment in strain GP1 appears to include a region of about 2.7 kb which harbors dhaA, dhaR, and part of invA (Fig. 2). The similarity of the dehalogenase gene region of strain GP1 to that of strain NCIMB13064 starts at nucleotide 17 of the invA ORF and ends exactly before the stop codon of the dhaA ORF (Fig. 3). This DNA segment in strain GP1 is identical to the corresponding segment in strain NCIMB13064, except for three nucleotide substitutions in dhaA and a 12-nucleotide deletion in the Rhodococcus regulatory gene dhaR. No further similarity was found between the two sequences. The haloalkane dehalogenase gene regions of the three phylogenetically different bacteria R. rhodochrous NCIMB13064, P. pavonaceae 170, and Mycobacterium sp. strain GP1 thus appear to have a common genetic origin. The globally distributed 1-chlorobutane catabolic gene cluster on plasmid pRTL1 (G. J. Poelarends, M. Zandstra, T. Bosma, L. A. Kulakov, M. J. Larkin, J. R. Marchesi, A. J. Weightman, and D. B. Janssen, submitted for publication) seems to be ancestral to the DNA fragments harboring the dhaA gene in strains 170 and GP1. These dhaA gene fragments probably originated from a catabolic gene cluster similar to the one present on pRTL1 in strain NCIMB13064 and were horizontally transferred to the present hosts. Since the structural genes are identical, we conclude that horizontal transfer of the dhaA gene fragment to strain 170 has occurred naturally and recently, resulting in the formation of a newly evolved pathway for 1,3-dichloropropene degradation (Fig. 1). The hydrolytic product of 1,3-dichloropropene, 3-chloroallyl alcohol, can be used as a carbon source by several gram-negative bacteria (5, 43). We also propose that the 1,2-dibromoethane-degrading pathway of strain GP1 arose by horizontal transfer of a DNA fragment harboring dhaA from a donor strain present in the original mixed enrichment culture to a 2-bromoethanol-degrading host. The host that obtained a complete degradation pathway for 1,2-dibromoethane in this way gained a selective advantage and became the predominant organism in the mixed culture.The role of the dhaR gene in the regulation of
dhaA expression.
The sequence analysis indicated that
expression of the dhaA gene in R. rhodochrous
NCIMB13064 may be regulated by the dhaR gene product. If
dhaR encodes a regulatory protein, its inactivation should
lead to either constitutive expression or noninducibility of the
dhaA gene, depending on the negative or positive nature of
the regulation, respectively. E. coli HB101 harboring
recombinant cosmid pLTL1k, which carried intact dhaR and
dhaA genes (Fig. 5),
constitutively expressed dhaA (Table
2), suggesting that expression of
dhaA is not regulated in E. coli. Introduction of pLTL1k into Pseudomonas sp. strain GJ1 did not lead to
constitutive expression of dhaA. We therefore used strain
GJ1 to analyze the role of the dhaR gene in the regulation
of dhaA expression.
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In strains 170 and GP1, a putative DNA integrase gene is present next to the conserved dhaA gene fragment. The sequence comparisons indicated that novel catabolic pathways for 1,3-dichloropropene and 1,2-dibromoethane were built by adding existing DNA fragments harboring dhaA to the genomes of P. pavonaceae 170 and Mycobacterium sp. strain GP1, respectively. This suggests the involvement of a mechanism for the acquisition of distinct DNA fragments. Gene acquisition by bacterial genomes could occur either by excisive-integrative recombination events mediated by insertion elements or by site-specific integration events mediated by DNA integrases (40, 42, 47).
Interestingly, an ORF encoding a putative DNA integrase (intP) was found upstream of the conserved dhaA gene fragment in strain 170 (Fig. 2 and Table 1). IntP shares significant similarity with proteins belonging to the integrase (Int) family of site-specific recombinases (Fig. 6A). Although the members of the Int family exhibit a large diversity in their sequences, they all harbor two regions of marked sequence similarity, called box I and box II (27). IntP shows 55% identity to its nearest neighbor, the integrase-like protein of Selenomonas ruminantium, in these two conserved domains (Fig. 6A). The tetrad R-H-R-Y, which includes the active-site tyrosine (31), is conserved in almost all members of the Int family (1, 4, 27) and is present as Arg-183, His-327, Arg-330, and Tyr-362 in IntP.
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The presence of insertion elements in the vicinity of the conserved dhaA gene fragments. Many catabolic genes are associated with transposons (42, 47), and transposition is clearly a major mechanism for the acquisition of catabolic genes by bacterial genomes. Sequence analysis of the regions (>4 kb) adjacent to the conserved dhaA gene fragment in Mycobacterium sp. strain GP1 showed that these regions do not encode any proteins related to known transposases. Distal to the dhaA gene fragment in P. pavonaceae 170, however, a large ORF (tnpA) was found (Fig. 2) of which the deduced amino acid sequence showed extensive similarity with the putative transposase of Pseudomonas pseudoalcaligenes JS45 (Table 1). The tnpA ORF, however, appeared to be interrupted by an insertion element, identified as IS1071 (Fig. 2), causing a truncation of its product. Nucleotide sequencing of a 1.7-kb fragment of IS1071 revealed no differences with the known sequence of IS1071, which is involved in transposition of the chlorobenzoate genes (26). PCR amplification, using a primer specific for both ends of IS1071 (due to the inverted repeats at its termini) and recombinant cosmid pPC33 as template DNA, showed the formation of a 3.2-kb PCR product corresponding to the size of IS1071 (26). Thus, a complete copy of IS1071 was present as an insertion in the tnpA gene approximately 1.6 kb downstream of dhaA.
Southern hybridization analysis revealed five copies of IS1071 in strain 170 but only two copies in strain 170M4, a spontaneous mutant of strain 170 that has lost the dhaA gene (35) (results not shown). The 60-kb plasmid pPC170, that was previously identified in strain 170 (44), is still present in strain 170M4, showing that the dhaA gene is not plasmid localized. Assuming that the mutation in strain 170M4 was caused by a single deletion event, this could suggest that the dhaA gene region in strain 170 is flanked by several copies of IS1071, forming a composite class I element, and that a homologous recombination event between two insertion sequences was responsible for the loss of the dhaA gene and three copies of IS1071. Strain 170M4 also lacked the integrase gene intP, which is consistent with such a deletion event. Many antibiotic resistance genes found on transposons in gram-negative bacteria are located within a conserved DNA sequence (15, 25, 40). These conserved elements, called integrons (16, 40), are formally distinct from other genetic elements in that they determine site-specific integration functions, a DNA integrase and a recombination site, and are thus able to acquire resistance genes at the specific site without the need for the presence of insertion sequences or integrase genes in the DNA segments that are acquired. If the integrase gene intP in P. pavonaceae 170 is flanked by IS1071 sequences and confers on this transposon a capability of taking up individual and unrelated catabolic genes by integrase-mediated recombination, strain 170 may possess a mobile DNA element similar to the previously identified integrons which are capable of taking up antibiotic resistance genes (16, 40). No sequences similar to IS1071 were found in strains NCIMB13064 and GP1, indicating that this insertion element was not involved in distribution of the dhaA gene among these strains. Similarly, insertion sequence IS2112, which is located approximately 6 kb upstream of the dhaA gene in strain NCIMB13064 (Fig. 2) (21), is not present in strains 170 and GP1. These results are consistent with the hypothesis that site-specific integration events mediated by IntP and IntM were responsible for the acquisition of the dhaA gene fragments, rather than excisive-integrative recombination events mediated by insertion elements. However, the presence of multiple copies of an active mobile element (IS1071) around the dhaA gene in strain 170, combined with the fact that strain 170 was recently isolated from a 1,3-dichloropropene-contaminated environment in which natural genetic exchange is likely to be important (44), suggests that transposition has played a part in the mobilization of the dhaA gene among members of the microbial community present in this environment.Concluding remarks. Our data provide further support for previous studies suggesting that horizontal transfer of genes involved in pollutant biodegradation may play an important role in the evolution of catabolic pathways and the adaptation of microbial communities to different environmental contaminants. Up to now, catabolic genes were thought to be transferred mainly by means of conjugative plasmids and transposons (42, 47). The results presented here suggest that genes specifying adaptation to xenobiotics can also spread as integrons, as has been proposed in the case of genes specifying antibiotic resistance (16, 40). The widespread use of antibiotics and the introduction of xenobiotics into the environment seem to lead to adaptation by similar molecular mechanisms.
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ACKNOWLEDGMENTS |
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This study was supported by the Life Sciences Foundation (SLW), which is subsidized by the Netherlands Organization for Scientific Research (NWO), and by the EC Environment and Climate Research Program contract ENV4-CT95-0086.
We thank P. Terpstra (BioMedical Technology Centre, University of Groningen, Groningen, The Netherlands) for his assistance in DNA sequencing and analysis.
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FOOTNOTES |
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* Corresponding author. Mailing address: Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands. Phone: 31-50-3634209. Fax: 31-50-3634165. E-mail: d.b.janssen{at}chem.rug.nl.
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REFERENCES |
|---|
|
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Abstract
Introduction
Materials and Methods
Results and Discussion
References
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|---|
| 1. |
Abremski, K. E., and R. H. Hoess.
1992.
Evidence for a second conserved arginine residue in the integrase family of recombination proteins.
Protein Eng.
5:87-91 |
| 2. | Albertini, A. M., M. Hofer, M. P. Calos, and J. H. Miller. 1982. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell 29:319-328[CrossRef][Medline]. |
| 3. |
Altschul, S. F.,
T. L. Madden,
A. A. Schäffer,
J. Zhang,
Z. Zhang,
W. Miller, and D. J. Lipman.
1997.
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Res.
25:3389-3402 |
| 4. | Argos, P., A. Landy, K. Abremski, J. B. Egan, E. Haggard-Ljungquist, R. H. Hoess, et al. 1986. The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J. 5:433-440[Medline]. |
| 5. |
Belser, N. O., and C. E. Castro.
1971.
Biodehalogenation  the metabolism of the nematocides cis- and trans-3-chloroallyl alcohol by a bacterium isolated from soil.
J. Agric. Food Chem.
19:23-26[CrossRef][Medline].
|
| 6. | Blatter, E. E., D. P. Abriola, and R. Pietruszko. 1992. Aldehyde dehydrogenase. Covalent intermediate in aldehyde dehydrogenation and ester hydrolysis. Biochem. J. 282:353-360. |
| 7. | Boyer, H. W., and D. Roulland-Dussoix. 1969. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J. Mol. Biol. 41:459-472[CrossRef][Medline]. |
| 8. | Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544[CrossRef][Medline]. |
| 9. |
Curragh, H.,
O. Flynn,
M. J. Larkin,
T. M. Stafford,
J. T. G. Hamilton, and D. B. Harper.
1994.
Haloalkane degradation and assimilation by Rhodococcus rhodochrous NCIMB13064.
Microbiology
140:1433-1442 |
| 10. | Dodd, I. B., and J. B. Egan. 1987. Systematic method for the detection of potential 8 Cro-like DNA-binding regions in proteins. J. Mol. Biol. 194:557-564[CrossRef][Medline]. |
| 11. |
Eaton, R. W.
1996.
p-Cumate catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA carrying the cmt operon.
J. Bacteriol.
178:1351-1362 |
| 12. | Farrés, J., T. T. Y. Wang, S. J. Cunningham, and H. Weiner. 1995. Investigation of the active site cysteine residue of rat liver mitochondrial aldehyde dehydrogenase by site-directed mutagenesis. Biochemistry 34:2592-2598[CrossRef][Medline]. |
| 13. |
Finan, T. M.,
B. Kunkel,
G. F. De Vos, and E. R. Signer.
1986.
Second symbiotic megaplasmid in Rhizobium meliloti carrying exopolysaccharide and thiamine synthesis genes.
J. Bacteriol.
167:66-72 |
| 14. | Glasgow, A. C., K. T. Hughes, and M. I. Simon. 1989. Bacterial DNA inversion systems, p. 637-659. In D. E. Berg, and M. M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C. |
| 15. | Hall, R. M., D. E. Brookes, and H. W. Stokes. 1991. Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point. Mol. Microbiol. 5:1941-1959[Medline]. |
| 16. | Hall, R. M., and H. W. Stokes. 1993. Integrons: novel DNA elements which capture genes by site-specific recombination. Genetica (The Hague) 90:115-132. |
| 17. | Janssen, D. B., A. Scheper, and B. Witholt. 1984. Biodegradation of 2-chloroethanol and 1,2-dichloroethane by pure bacterial cultures. Prog. Ind. Microbiol. 20:169-178. |
| 18. |
Janssen, D. B.,
F. Pries,
J. Van der Ploeg,
B. Kazemier,
P. Terpstra, and B. Witholt.
1989.
Cloning of 1,2-dichloroethane degradation genes of Xanthobacter autotrophicus GJ10 and expression and sequencing of the dhlA gene.
J. Bacteriol.
171:6791-6799 |
| 19. | Keen, N. T., S. Tamaki, D. Kobayashi, and D. Trollinger. 1988. Improved broad-host-range plasmids for DNA cloning in Gram-negative bacteria. Gene 70:191-197[CrossRef][Medline]. |
| 20. |
Keuning, S.,
D. B. Janssen, and B. Witholt.
1985.
Purification and characterization of hydrolytic haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.
J. Bacteriol.
163:635-639 |
| 21. | Kulakov, L. A., G. J. Poelarends, D. B. Janssen, and M. J. Larkin. 1999. Characterization of IS2112, a new insertion sequence from Rhodococcus, and its relationship with mobile elements belonging to the IS110 family. Microbiology 145:561-568[CrossRef][Medline]. |
| 22. | Kulakova, A. N., T. M. Stafford, M. J. Larkin, and L. A. Kulakov. 1995. Plasmid pRTL1 controlling 1-chloroalkane degradation by Rhodococcus rhodochrous NCIMB13064. Plasmid 33:208-217[CrossRef][Medline]. |
| 23. |
Kulakova, A. N.,
M. J. Larkin, and L. A. Kulakov.
1997.
The plasmid-located haloalkane dehalogenase gene from Rhodococcus rhodochrous NCIMB13064.
Microbiology
143:109-115 |
| 24. | Larkin, M. J., R. De Mot, L. A. Kulakov, and I. Nagy. 1998. Applied aspects of Rhodococcus genetics. Antonie Leeuwenhoek 74:133-153. |
| 25. | Martinez, E., and F. De la Cruz. 1990. Genetic elements involved in Tn21 site-specific integration, a novel mechanism for the dissemination of antibiotic resistance genes. EMBO J. 9:1275-1281[Medline]. |
| 26. |
Nakatsu, C.,
J. Ng,
R. Singh,
N. Straus, and C. Wyndham.
1991.
Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences.
Proc. Natl. Acad. Sci. USA
88:8312-8316 |
| 27. |
Nunes-Düby, S. E.,
H. J. Kwon,
R. S. Tirumalai,
T. Ellenberger, and A. Landy.
1998.
Similarity and differences among 105 members of the Int family of site-specific recombinases.
Nucleic Acids Res.
26:391-406 |
| 28. |
Okamoto, S.,
K. Nakamura,
T. Nihira, and Y. Yamada.
1995.
Virginiae butanolide binding protein from Streptomyces virginiae: evidence that VbrA is not the virginiae butanolide binding protein and reidentification of the true binding protein.
J. Biol. Chem.
270:12319-12326 |
| 29. |
Onaka, H.,
N. Ando,
T. Nihira,
Y. Yamada,
T. Beppu, and S. Horinouchi.
1995.
Cloning and characterization of the A-factor receptor gene from Streptomyces griseus.
J. Bacteriol.
177:6083-6092 |
| 30. | Pabo, C. O., and R. T. Sauer. 1984. Protein-DNA recognition. Annu. Rev. Biochem. 53:293-321[CrossRef][Medline]. |
| 31. |
Pargellis, C. A.,
S. E. Nunes-Düby,
L. M. De Vargas, and A. Landy.
1988.
Suicide recombination substrates yield covalent lambda integrase-DNA complexes and lead to identification of the active site tyrosine.
J. Biol. Chem.
263:7678-7685 |
| 32. |
Park, D. H., and B. V. Plapp.
1991.
Isoenzymes of horseliver alcohol dehydrogenase active on ethanol and steroids. cDNA cloning, expression, and comparison of active sites.
J. Biol. Chem.
266:13296-13302 |
| 33. | Persson, B., T. Bergman, W. M. Keung, U. Waldenstrom, B. Holmquist, B. L. Vallee, and H. Jornvall. 1993. Basic features of class-I alcohol dehydrogenase: variable and constant segments coordinated by inter-class and intra-class variability. Conclusions from characterization of the alligator enzyme. Eur. J. Biochem. 216:49-56[Medline]. |
| 34. |
Plasterk, R. H.,
A. Brinkman, and P. Van de Putte.
1983.
DNA inversions in the chromosome of Escherichia coli and in bacteriophage Mu: relationship to other site-specific recombination systems.
Proc. Natl. Acad. Sci. USA
80:5355-5358 |
| 35. |
Poelarends, G. J.,
M. Wilkens,
M. J. Larkin,
J. D. Van Elsas, and D. B. Janssen.
1998.
Degradation of 1,3-dichloropropene by Pseudomonas cichorii 170.
Appl. Environ. Microbiol.
64:2931-2936 |
| 36. |
Poelarends, G. J.,
J. E. T. van Hylckama Vlieg,
J. R. Marchesi,
L. M. Freitas dos Santos, and D. B. Janssen.
1999.
Degradation of 1,2-dibromoethane by Mycobacterium sp. strain GP1.
J. Bacteriol.
181:2050-2058 |
| 37. | Reid, M. F., and C. A. Fewson. 1994. Molecular characterization of microbial alcohol dehydrogenases. Crit. Rev. Microbiol. 20:13-56[Medline]. |
| 38. | Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. |
| 39. |
Staskawicz, B.,
D. Dahlbeck,
N. Keen, and C. Napoli.
1987.
Molecular characterization of cloned avirulence genes from race 0 and race 1 of Pseudomonas syringae pv. glycinea.
J. Bacteriol.
169:5789-5794 |
| 40. | Stokes, H. W., and R. M. Hall. 1989. A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol. Microbiol. 3:1669-1683[Medline]. |
| 41. |
Thompson, J. D.,
D. G. Higgens, and T. J. Gibson.
1994.
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic Acids Res.
22:4673-4680 |
| 42. | Tschäpe, H. 1994. The spread of plasmids as a function of bacterial adaptability. FEMS Microbiol. Ecol. 15:23-32. |
| 43. |
Van der Waarde, J. J.,
R. Kok, and D. B. Janssen.
1993.
Degradation of 2-chloroallyl alcohol by a Pseudomonas sp.
Appl. Environ. Microbiol.
59:528-535 |
| 44. | Verhagen, C., E. Smit, D. B. Janssen, and J. D. Van Elsas. 1995. Bacterial dichloropropene degradation in soil; screening of soils and involvement of plasmids carrying the dhlA gene. Soil Biol. Biochem. 27:1547-1557[CrossRef]. |
| 45. |
Waki, M.,
T. Nihira, and Y. Yamada.
1997.
Cloning and characterization of the gene (farA) encoding the receptor for an extracellular regulatory factor (IM-2) from Streptomyces sp. strain FRI-5.
J. Bacteriol.
179:5131-5137 |
| 46. | Willuhn, J., H. P. Schmitt-Wrede, A. Otto, and F. Wunderlich. 1996. Cadmium-detoxification in the earthworm Enchytraeus: specific expression of a putative aldehyde dehydrogenase. Biochem. Biophys. Res. Commun. 226:128-134[CrossRef][Medline]. |
| 47. | Wyndham, R. C., A. E. Cashore, C. H. Nakatsu, and M. C. Peel. 1994. Catabolic transposons. Biodegradation 5:323-342[CrossRef][Medline]. |
| 48. | Xia, X., A. R. W. Smith, and I. J. Bruce. 1996. Identification and sequencing of a novel insertion sequence, IS1471, in Burkholderia cepacia strain 2a. FEMS Microbiol. Lett. 144:203-206[CrossRef][Medline]. |
| 49. | Yanisch-Perron, C., J. Vieira, and J. Messing. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-109[CrossRef][Medline]. |
| 50. | Yu, F., T. Nakamura, W. Mizunashi, and I. Watanabe. 1994. Cloning of two halohydrin halogen-halide lyase genes from Corynebacterium sp. strain N-1074 and structural comparison of the genes and gene products. Biosci. Biotechnol. Biochem. 58:1451-1457[Medline]. |
| 51. |
Zieg, J., and M. Simon.
1980.
Analysis of the nucleotide sequence of an invertable controlling element.
Proc. Natl. Acad. Sci. USA
77:4196-4200 |
Journal of Bacteriology, April 2000, p. 2191-2199, Vol. 182, No. 8
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