Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, D-48149 Münster, Germany
Correspondence
Susanne Fetzner
fetzner{at}uni-muenster.de
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ABSTRACT |
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*These authors contributed equally to this work.
Present address: Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand.
Present address: Institut für Molekulare Infektionsbiologie, Universität Würzburg, Germany.
The GenBank/EMBL/DDBJ accession numbers for the nucleotide sequences of the 16S rDNA of strains Rü61a, B2-6, KA1-1, KA4-2, K2-29 and OF11 determined in this study are AJ785758, AJ785759, AJ785760, AJ785761, AJ785762 and AJ785763, respectively.
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INTRODUCTION |
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Arthrobacter nitroguajacolicus strain Rü61a (formerly assigned to the species Arthrobacter ilicis) utilizes quinaldine (2-methylquinoline), a constituent of coal tar, as sole source of carbon and energy (Hund et al., 1990). Degradation via the anthranilate pathway (Fig. 1
) is initiated by the oxidation of quinaldine to 1H-4-oxoquinaldine, catalysed by quinaldine 4-oxidase (Qox). 1H-4-oxoquinaldine 3-monooxygenase subsequently generates 1H-3-hydroxy-4-oxoquinaldine, which undergoes 2,4-dioxygenolytic ring cleavage to form carbon monoxide and N-acetylanthranilate. This unusual mode of ring cleavage is catalysed by a cofactor-less 2,4-dioxygenase that does not share any similarity with aromatic ring cleavage dioxygenases, but seems to belong to the
/
-hydrolase fold superfamily of proteins (Fetzner, 2002
). In the next step, an amidase (Amq) catalyses the hydrolysis of N-acetylanthranilate to anthranilate. We have characterized the gene cluster encoding this upper part of the degradation pathway (Parschat et al., 2003
); however, the genes of anthranilate utilization by strain Rü61a have not been identified so far.
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A number of bacteria within the order Actinomycetales contain linear plasmids which encode catabolic traits (Dabrock et al., 1994; Kosono et al., 1997
; Shimizu et al., 2001
; Coleman & Spain, 2003
; König et al., 2004
), hydrogen autotrophy (Kalkus et al., 1990
), determinants of virulence (Crespi et al., 1992
), heavy metal resistance (Dabrock et al., 1994
; Ravel et al., 1998
; Stecker et al., 2003
) or the production of secondary metabolites (Kinashi et al., 1987
; Suwa et al., 2000
). Linear plasmids have been described to occur in species of Streptomyces (Hayakawa et al., 1979
; Kinashi et al., 1987
; Chen et al., 1993
; Kinoshita-Iramina et al., 1997
; Suwa et al., 2000
; Spatz et al., 2002
), Rhodococcus (Crespi et al., 1992
; Kalkus et al., 1990
; Kosono et al., 1997
; Shimizu et al., 2001
; Stecker et al., 2003
; König et al., 2004
), Mycobacterium (Picardeau & Vincent, 1997
, 1998
; Le Dantec et al., 2001
; Coleman & Spain, 2003
), Planobispora (Polo et al., 1998
) and Clavibacter (Brown et al., 2002
). The size of these linear replicons ranges from 11·7 to more than 600 kb, and most of them have been shown to be capable of conjugative transfer (Meinhardt et al., 1997
; Picardeau & Vincent, 1998
; Ravel et al., 2000
). However, in Arthrobacter spp. linear plasmids have not yet been reported.
Based on the observation that mutants unable to grow on quinaldine occur spontaneously when A. nitroguajacolicus Rü61a is grown in complex medium, we hypothesized that genes encoding quinaldine degradation might be localized on a plasmid. As our attempts to detect a circular plasmid failed, we searched for linear extrachromosomal elements. Here we report on the identification of a linear catabolic megaplasmid in A. nitroguajacolicus Rü61a, designated pAL1, and provide evidence that the upper part of the anthranilate pathway of quinaldine degradation is encoded by pAL1. Five other quinaldine-degrading strains isolated from soil were found to belong to the genus Arthrobacter, and four of them contain a very similar, if not identical, plasmid.
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METHODS |
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Arthrobacter strains were grown in mineral salts medium (Stephan et al., 1996) with 1 g (NH4)2SO4 l1 and vitamin solution (1 ml l1) (Röger et al., 1990
), containing 4 or 2 mM quinaldine or 2 mM L-nicotine as carbon sources, or in nutrient broth yeast extract (NBYE) medium (Gartemann & Eichenlaub, 2001
) or in Lysogeny Broth (LB) (Sambrook et al., 1989
; Bertani, 2004
) at 30 °C. Gram staining of the isolates was performed with the Gram staining kit from Fluka.
A. nitroguajacolicus Rü61a pAL1 (RifR StrR) was obtained by repeated transfer of A. nitroguajacolicus Rü61a (RifR StrR) in LB and selection for loss of quinaldine utilization. Elimination of pAL1 from the genome was confirmed by PFGE and hybridization with pAL1-specific probes.
Plasmid pKGT452C (Gartemann & Eichenlaub, 2001
), kindly supplied by R. Eichenlaub, was propagated in the methylase-negative strain Escherichia coli ET12567 (MacNeil et al., 1992
) grown at 37 °C in LB containing ampicillin (100 µg ml1) and chloramphenicol (50 µg ml1). Arthrobacter strains carrying the transposon Tn1409C
were grown in the presence of 10 µg chloramphenicol ml1. E. coli DH5
(Woodcock et al., 1989
), used for cloning of an intergenic fragment of pAL1 and related plasmids, was grown in LB containing 100 µg ampicillin ml1 when harbouring pUC18 derivatives.
DNA techniques.
Genomic DNA of Arthrobacter strains was isolated according to the method of Rainey et al. (1996). Plasmid DNA from E. coli strains was isolated with the Qiagen Plasmid Mini kit. DNA restriction and agarose gel electrophoresis were carried out using standard procedures (Sambrook et al., 1989
).
The 16S rRNA gene was amplified from total DNA using the oligonucleotide primers GM3F and GM4R (Muyzer et al., 1995). A 478 bp intergenic region that is located downstream of ORF5 in pAL1 (Parschat et al., 2003
) was amplified using the primers frag-up (5'-AAGTATCACCAGCTCACTGG-3') and frag-down (5'-ATCAGCACTCGCTCACCAAGGTTC-3'), and total DNA of quinaldine-degrading strains as templates. Fragments were ligated into pUC18 (Vieira & Messing, 1982
) and cloned in E. coli DH5
. PCR products were purified with the High Pure PCR Purification Kit (Roche Applied Science). DNA sequencing was performed with a 4000L DNA sequencer (LI-COR Inc., Biotechnology Division) using the dideoxy chain-termination method (Sanger et al., 1977
). The CycleReader Auto Sequencing Kit (Fermentas) was used as specified by the manufacturer, together with oligonucleotide primers labelled with the synthetic fluorescent dye IRD800. For both the 16S rRNA genes and the intergenic regions, sequencing of both strands was done at least in duplicate.
Chloramphenicol resistant (CmR) transposon mutants of a spontaneous RifR StrR mutant of A. nitroguajacolicus Rü61a pAL1 and of A. nicotinovorans DSM 420 were obtained by electroporation of competent cells with the plasmid pKGT452C isolated from E. coli ET12567 as described by Gartemann & Eichenlaub (2001)
. The presence of the cmx gene encoding a chloramphenicol exporter protein in the genome of these mutants was verified by PCR using the primer cmx-up (5'-CGCGGGATTGCTCCCCGCGATC-3') and cmx-down (5'-GGTCGCGAGCCCGAGCGCACCAAG-3'), and genomic DNA as template.
The 16S rDNA sequences were aligned with published sequences from representative Arthrobacter species from the National Center for Biotechnology Information (NCBI) database. A phylogenetic tree of the quinaldine-degrading strains, different Arthrobacter spp. and the type strain of Kocuria rosea (DSM 20447) was constructed based on a sequence consensus length of 1427 nt of 16S rDNA (excluding gaps and Ns from the analysis). The fastDNAml program (Olsen et al., 1994) within the PAUP* 4.0 software (Swofford, 2002
), which uses a maximum-likelihood approach, was used for the phylogenetic analysis. Binary alignments of the 16S rDNA sequences were performed with the program BestFit (Smith & Waterman, 1981
).
DNA probes and Southern hybridization.
DNA separated in agarose gels by PFGE was transferred by vacuum-blotting to nylon membranes (Porablot NY Plus; Macherey-Nagel). Specific probes for the plasmid-localized genes amq (encoding Amq) and qoxL (encoding the large subunit of Qox) corresponded to nt 1394114651 and 1749021400, respectively, of the sequence deposited under EMBL accession no. AJ537472. The probes were labelled with a digoxigenin derivative, using the DIG-High Prime DNA Labelling Kit (Roche Applied Science). Prehybridization, hybridization and colorimetric detection were performed following The DIG System User's Guide for Filter Hybridization (Boehringer Mannheim, 1995).
Preparation of cell plugs, PFGE and isolation of linear plasmid DNA.
Cell plugs for PFGE were prepared by modifying the method described by Schenk et al. (1998). Cells of Arthrobacter spp. were grown either in mineral salts medium containing quinaldine or in LB to an OD600 of 22·5. The washed bacterial cell pellets were preincubated in PIV buffer (1 M NaCl, 1 mM Tris/HCl, pH 7·6) containing 1 mg lysozyme ml1 (37 °C, 15 min). Cells were embedded in low-melting-point agarose, lysed using the method of Schenk et al. (1998)
and equilibrated in TE buffer (10 mM Tris/HCl, 1 mM EDTA, pH 8). Subsequent proteinase K treatment of the agarose plugs (if appropriate) was performed as described by Schenk et al. (1998)
; however, the samples were incubated for 5 h at 50 °C instead of overnight. PFGE was carried out in a contour-clamped homogeneous electric field apparatus (CHEF-DR III; Bio-Rad) using broad range agarose (1 %, w/v, gels). Electrophoresis was performed at 5 V cm1 and 14 °C. The pulse time increased from 10 to 50 s, or from 40 to 90 s, during a 16 or 17 h run, respectively. Concatemers of
DNA were used as size standard (Lambda DNA Ladder in InCert Agarose Gel Plugs; CAMBREX UK). To isolate pAL1, the relevant DNA band was excised from pulsed field (PF) agarose gels and the DNA was obtained by electroelution followed by precipitation with ethanol.
S1 nuclease and exonuclease treatment of pAL1.
For treatment with S1 nuclease, agarose plugs with lysed cells of A. nitroguajacolicus Rü61a, or cell plugs after lysis and proteinase K treatment, were washed twice in S1 nuclease buffer (40·5 mM potassium acetate, 338 mM NaCl, 1·3 mM ZnSO4, 6·8 %, w/v, glycerol, pH 7·0) and incubated with 20 or 50 Units S1 nuclease ml1 for 45 min at 37 °C. The reaction was stopped by adding 10 mM EDTA and cooling to 4 °C. Control experiments were performed without S1 nuclease. Plugs with lysed cells of strain Rü61a, treated with S1 nuclease, were washed in TE buffer and subsequently incubated for 2 h with 5, 10 or 20 Units exonuclease to examine if S1 nuclease treatment leads to the formation of unprotected 5' ends.
To assess the sensitivity of proteinase-K-treated pAL1 DNA to exonucleases, plasmid DNA isolated from a preparative PF gel was embedded in an equal volume of 1 % (w/v) low-melting-point agarose to prepare plugs containing approximately 100 ng plasmid DNA, and treated as described by Kalkus et al. (1993); however, 50 Units exonuclease III and 5 Units
exonuclease were used. Remaining single-stranded plasmid DNA was removed by adding 0·6 Units mung bean nuclease ml1 and incubation at 37 °C for 30 min. For termination of the reaction, the buffer was replaced by TE buffer.
Analysis of the degradative potential of A. nitroguajacolicus Rü61a pAL1.
To determine the ability of A. nitroguajacolicus Rü61a pAL1 to use quinaldine or intermediates of the anthranilate pathway as carbon and energy source, the carbon sources were added to the medium in concentrations of 0·1 % (w/v) for 1H-4-oxoquinaldine, N-acetylanthranilate and anthranilate, and 0·05 % (v/v) for quinaldine. Mineral salts medium was inoculated with 3 % (v/v) of an overnight culture in LB. Degradation of the substrates was monitored spectrophotometrically in the culture supernatant. Spectra were compared with those of authentic references diluted in the same medium.
Mating experiments.
Filter mating was performed using A. nitroguajacolicus Rü61a as the donor, and the transposon mutants A. nitroguajacolicus Rü61a pAL1 RifR StrR CmR and A. nicotinovorans DSM 420 CmR as recipients. Filters containing a mixture of donor and recipient cells at a 1 : 1 ratio were incubated for 24 h at 30 °C on the surface of an LB agar plate. Then the cells were suspended in 1 ml saline (0·9 % NaCl) and appropriate portions were spread onto agar plates of mineral salts medium with 2 mM quinaldine as sole source of carbon and energy, and 10 µg chloramphenicol ml1.
To detect pAL1 in transconjugants, the amq gene, which is localized on pAL1, was amplified by PCR using the primer pair ORF4-up (5'-AAGGATGCTAAGCGAAGTGCTC-3') and ORF4-down (5'-TGATGGCAAACCTCACCAAGAC-3'). In A. nicotinovorans DSM 420 CmR transconjugants, the presence of pAO1 (Igloi & Brandsch, 2003) was shown by amplifying part of the 6hlno gene (EMBL accession no. AJ507836) using the primer 6hlno-up (5'-GGCATTTCCTATTCCTGGCTCA-3') and 6hlno-down (5'-GCTCTCCAAGTTCCTTATGCACTC-3'). The gene encoding 6-hydroxy-L-nicotine oxidase (6HLNO) is part of the gene cluster involved in nicotine degradation encoded by pAO1 (Igloi & Brandsch, 2003
).
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RESULTS AND DISCUSSION |
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Proteins are attached to the 5' ends of pAL1
In contrast to the native plasmid from cells lysed without any proteinase or nuclease treatment (Fig. 2a, lane 1), pAL1 molecules migrated into the PF gel after treatment of the cell plugs with proteinase K (Fig. 2a
, lane 3) or SDS (not shown), suggesting that proteins are attached to the DNA. The terminal proteins of linear replicons of streptomycetes and other actinomycetes were previously proposed to be covalently bound to the 5' ends (Kalkus et al., 1993
; Ravel et al., 1998
; Polo et al., 1998
; Yang et al., 2002
; Stecker et al., 2003
). As a consequence, the linear plasmid is insensitive to 5'3' exonuclease, but sensitive to 3'5' exonuclease.
pAL1 was isolated from a preparative PF gel and tested for sensitivity to E. coli exonuclease III and phage exonuclease, which hydrolyse dsDNA in the 3'5' and 5'3' directions, respectively. As shown in Fig. 3
, DNA exonuclease III completely degraded pAL1, whereas
exonuclease did not, indicating that the 5' end of pAL1 is protected, even after proteinase K treatment. The functionality of the
exonuclease was proven by digestion of pUC18 plasmid DNA linearized with SmaI (not shown). The result is consistent with the proposal of a covalent bond between the 5' end and the terminal protein which is not hydrolysed by proteinase K. For Streptomyces linear replicons, attachment of the 5' phosphate to the hydroxyl group of a serine residue on the terminal protein has been suggested (Yang et al., 2002
).
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Quite surprisingly, treatment of lysed cells of strain Rü61a with S1 nuclease seemed to be sufficient for pAL1 to enter the PF gel (Fig. 2a, lane 2). Sequential treatment of embedded, lysed cells with S1 nuclease and
exonuclease indicated that the terminal proteins of pAL1 are not removed by S1 nuclease treatment. However, when plugs containing lysed cells after equilibration in TE buffer were incubated in S1 nuclease buffer without addition of the enzyme, pAL1 showed the same mobility in the PF gel as after incubation with S1 nuclease or after treatment with SDS. In contrast, pAL1 did not migrate into the PF gel when either ZnSO4 or NaCl was omitted from the S1 nuclease buffer, or when the salt concentration in the buffer was decreased to 50 or 200 mM NaCl. We suggest that S1 nuclease buffer has a denaturing effect on the terminal proteins of pAL1. When the soluble protein fraction of crude extracts of A. nitroguajacolicus Rü61a was incubated in this buffer for 45 min at 4 and 37 °C, about 40 and 50 % of the total protein was precipitated, respectively, demonstrating the potential of the buffer as a denaturant for proteins.
pAL1 encodes quinaldine conversion to anthranilate
We previously showed that a 10·8 kb HindIII fragment of DNA from A. nitroguajacolicus Rü61a contains the genes encoding the enzymes of the upper part of the anthranilate pathway of quinaldine degradation, i.e. the conversion of quinaldine to anthranilate (Fig. 1) (Parschat et al., 2003
). Southern blotting following PFGE and hybridization with a probe specific for amq (Fig. 2b
) and with a qoxL-specific probe showed that this 10·8 kb fragment is actually part of pAL1. A mutant that spontaneously had lost the ability to utilize quinaldine, 1H-4-oxoquinaldine and N-acetylanthranilate was analysed by PFGE and Southern hybridization. pAL1 indeed was not detected in the mutant and the genomic DNA did not show hybridization signals with probes specific for the qoxL and amq genes (Fig. 4
), confirming that the enzymes involved in anthranilate formation from quinaldine are encoded by the plasmid and were lost in the mutant. However, A. nitroguajacolicus Rü61a pAL1 was able to grow on anthranilate, indicating that a pathway for anthranilate utilization is chromosomally encoded. The anthranilate metabolism of strain Rü61a was previously proposed to proceed via catechol and the ortho cleavage pathway (Hund et al., 1990
).
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Most of the linear plasmids identified in Actinomycetes were reported to be transmissible plasmids (Meinhardt et al., 1997; Picardeau & Vincent, 1998
; Ravel et al., 2000
). Plasmid-mediated conjugation probably enables these soil bacteria to share advantageous genetic elements. Linear conjugative replicons such as pAL1, pBD2 of R. erythropolis BD2 encoding isopropylbenzene catabolism (Dabrock et al., 1994
; Stecker et al., 2003
), the linear plasmids of rhodococci involved in polychlorinated biphenyl degradation (Shimizu et al., 2001
; Kosono et al., 1997
) or those of alkene-assimilating Mycobacterium strains (Coleman & Spain, 2003
) may play an important role in the dissemination of catabolic capabilities and may be important for the evolution of degradation pathways.
The quinaldine-degrading strains belong to the genus Arthrobacter, and four out of five new isolates contain a pAL1-like plasmid
All quinaldine-degrading strains that were isolated from the soil samples were Gram-positive and 16S rDNA analysis suggested that they all belong to the genus Arthrobacter. Based on a sequence of 1432 nt, the highest similarity of the 16S rDNA of strain Rü61a was found with the 16S rRNA gene from A. nitroguajacolicus DSM 15232 (EMBL accession no. AJ512504) (99·9 % identity in the binary comparison), whereas binary alignments with 16S rDNA of A. ilicis DSM 20138 (EMBL accession no. AIRNA16S) and A. aurescens DSM 20116 (EMBL accession no. AARNA16S) revealed identities of 99·0 and 99·6 %, respectively. We thus suggest that strain Rü61a belongs to the species A. nitroguajacolicus rather than A. ilicis. Remarkably, the 16S rDNA sequences of strain OF11 and the acyl-homoserine lactone-utilizing strain Arthrobacter sp. VAI-A (Flagan et al., 2003) showed 99·9 % identity (comparison of 1431 nt). Fig. 5
shows the phylogenetic positions of the isolates compared to related Arthrobacter spp. and K. rosea.
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ACKNOWLEDGEMENTS |
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Received 28 July 2004;
revised 12 October 2004;
accepted 19 October 2004.
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