Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
Correspondence
Tamara Basta
tbasta{at}pasteur.fr
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ABSTRACT |
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Present address: Institut Pasteur, 25 Rue du Dr Roux, F-75724, Paris, France.
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INTRODUCTION |
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Previous reports demonstrated that in the naphthalene- and biphenyl-degrading strain Sphingomonas aromaticivorans F199 and in some naphthalenesulfonate-, dibenzofuran-, dibenzo-p-dioxin- or carbazole-degrading sphingomonads, the relevant degradative pathways are localized on rather large plasmids (Basta et al., 2004; Feng et al., 1997
; Ogram et al., 2000
; Romine et al., 1999
).
Currently, plasmid pNL1 from S. aromaticivorans F199 is the only plasmid from a Sphingomonas strain that has been sequenced, and it has been found that about one-third of the identified ORFs of this plasmid are associated with the catabolism or transport of aromatic compounds (Romine et al., 1999). S. aromaticivorans F199 has been isolated from a deep-subsurface location in the USA from a depth of about 400 m. This is a rather extraordinary niche for a micro-organism degrading organic compounds because these sediments are extremely poor in nutrients and thus the organisms have to survive under oligotrophic conditions (Fredrickson et al., 1999
).
In our recent study, we demonstrated that large plasmids are ubiquitous in xenobiotic-degrading sphingomonads and that they are important for the dissemination of degradative abilities among these organisms (Basta et al., 2004). We therefore decided to compare these plasmids, with regard to incompatibility grouping and organization of the degradative genes, with plasmid pNL1, in order to gain more information about the diversity and characteristics of Sphingomonas plasmids.
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METHODS |
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Molecular techniques for the manipulation of DNA.
Genomic DNA from Sphingomonas strains was prepared after SDS lysis and phenol extraction, as described elsewhere (Eulberg et al., 1997). The digestion of DNA with restriction endonucleases (New England Biolabs) and agarose gel electrophoresis were performed according to standard procedures (Sambrook et al., 1989
). The elution and purification of DNA from agarose gels was performed using the Easy Pure Kit as recommended by the manufacturer (Biozym).
Preparation of genomic DNA from sphingomonads for the detection of megaplasmids.
Plasmids were isolated and separated from chromosomal DNA using PFGE by the method of Barton et al. (1995), as described previously (Basta et al., 2004
).
PCR experiments.
All PCR experiments were performed using a Genius thermal cycler (Techne) in thin-walled 200 µl reaction tubes. The PCR reaction mixtures contained, in a volume of 30 µl, 200 ng DNA, 0·3 µM of each forward and reverse primer (Eurogentec), 10 mM Tris/HCl (pH 8·3), 50 mM KCl, 1·5 mM magnesium acetate, 0·2 mM dNTPs (Eppendorf) and 0·51 U Taq DNA polymerase (Eppendorf) under the conditions indicated below.
The primers for the detection of replicons with replicative functions similar to those of plasmid pNL1 were derived from the corresponding nucleotide sequence of plasmid pNL1 deposited at the NCBI database (Table 2). The following PCR programme was used for the amplification of the replicon regions from different sphingomonads: an initial denaturation (3 min, 94 °C) was followed by 30 cycles consisting of annealing at 60 °C (30 s), polymerization at 72 °C (40 s for the amplification of repAb homologues, 45 s for the amplification of DNA fragments containing iteron sequences, and 3 min for the amplification of the DNA region containing repAaAb), and denaturation at 94 °C (30 s). Finally, an additional polymerization step was performed at 72 °C for 5 min.
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The DNA fragments for the generation of the gene probes used for the detection of cluster 1, cluster 2 and cluster 3 were amplified by PCR using primer combinations Block1-B and Block1-C, Block2-A and Block2-F, and Block3-A and Block3-D, respectively (Table 2). The PCR conditions applied were the same as described above, except for the amplification of part of cluster 2. This fragment was amplified using the PCR program consisting of an initial denaturation (3 min, 95 °C), followed by 30 cycles of annealing at 62 °C (30 s), polymerization at 72 °C (4 min), and denaturation at 95 °C (30 s). The last polymerization step was extended to 10 min.
The arrangement of the conserved catabolic gene clusters in sphingomonads was determined using long-range PCR (LR-PCR) experiments. For amplification of long PCR products (520 kb), the Expand long template PCR system (Roche), containing a mixture of Taq polymerase and Pwo proofreading DNA polymerase, was used. The reaction mixtures contained 200500 ng template, and all other components in the concentrations suggested by the manufacturer. In some cases, 1 M betaine or 6 % (v/v) DMSO was added. The primers used in the LR-PCR experiments were derived from the published nucleotide sequences of catabolic gene clusters of S. xenophaga BN6 and S. aromaticivorans F199 (Table 2).
The PCR program used consisted of an initial denaturation step at 96 °C (6 min) followed by 10 cycles of denaturation at 94 °C (15 s), primer annealing at 6468 °C (30 s), polymerization at 68 °C (1215 min) and 20 cycles of denaturation at 94 °C (15 s), primer annealing at 6468 °C (30 s), polymerization at 68 °C (1215 min+20 s per cycle). The final polymerization step was prolonged to 8 min.
Hybridization procedures.
A DIG DNA labelling and detection kit was used according to the instructions of the supplier (Roche). The hybridization temperature in the experiments with the repA probes was set to 56 °C and, with the probes for the detection of the three conserved gene clusters, to 65 °C.
Sequence comparisons.
Standard sequence analysis, database searches and comparisons were done with the BLAST search facilities at the NCBI. The gene clusters from strains BN6 und F199 were aligned using the MEGALIGN module of the lasergene program (DNASTAR Inc.).
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RESULTS |
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PCR detection of conserved catabolic gene clusters in different naphthalene-, biphenyl- and toluene-degrading sphingomonads
The experiments described above suggested that S. subterranea and S. aromaticivorans B0695 harboured plasmids with similar replication functions to those of plasmid pNL1. These strains had been isolated at different depths (180407 m) from the same subsurface location as S. aromaticivorans F199 and also degraded a similar range of aromatic compounds (Fredrickson et al., 1995). Previous hybridization studies had demonstrated that in S. subterranea (=strain B0478), S. stygia (=strain B0712) and S. aromaticivorans B0695 the genes that are involved in the degradation of the aromatic compounds were localized on plasmids with sizes of about 130, 270, and 180 plus 800 kb, respectively (Balkwill et al., 1997
; Kim et al., 1996
). We therefore tested if the organization of the degradative genes in these strains resembled that of S. aromaticivorans F199.
The comparison of the genetic organization of the genes involved in the degradation of naphthalene/biphenyl/toluene and naphthalenesulfonates in strains F199 and BN6, respectively, indicated the conservation of three gene clusters in these strains. Recently, two of these clusters have also been reported for a phenanthrene-degrading sphingomonad (Sphingobium sp. strain P2) (Pinyakong et al., 2003) (Fig. 3
). These gene clusters shared significant nucleotide sequence identities ranging from 60 to 90 %. Specific pairs of oligonucleotide primers were derived for each gene cluster after comparison of the published nucleotide sequences from strains BN6 and F199 (Table 2
, Fig. 3
). Gene cluster 2 (see Fig. 3
) was rather large (5·2 kb). Therefore, three pairs of PCR primers were designed in order to specifically amplify parts of this cluster. The oligonucleotide primers used were positioned in such a manner that the DNA fragments generated by PCR overlapped and enclosed all the genes in the gene cluster (Fig. 3
). Thus, according to the sizes of the PCR products obtained, it was possible to deduce if the investigated strains encoded gene clusters similar to those found in strains F199 and BN6. The functionality of the deduced primers was shown in PCR experiments with the genomic DNA of S. aromaticivorans F199 as template. Thus, single PCR products of the expected sizes were obtained (Table 4
). These primer sets were then used to investigate the presence of the three conserved gene clusters in the deep-subsurface strains, and PCR products of the expected sizes were detected. This indicated that all three gene clusters were conserved in S. stygia, S. subterranea and S. aromaticivorans B0695 (Fig. 4
). In contrast, the conserved gene clusters could not be detected in the surface isolates Sphingomonas yanoikuyae B1, Sphingomonas paucimobilis Q1, and Sphingomonas sp. EPA505, which degrade a similar range of compounds as the subsurface strains. Furthermore, no PCR products were obtained with any of the PCR primers with the DNAs from S. paucimobilis, Sphingomonas chlorophenolica ATCC 33790 and Sphingomonas wittichii RW1.
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DISCUSSION |
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Naphthalene- and biphenyl-degrading Sphingomonas strains have also been isolated from surface locations, for example, S. paucimobilis Q1, S. yanoikuyae B1, and Sphingomonas sp. EPA505 (Furukawa et al., 1989; Mueller et al., 1997
; Yabuuchi et al., 1990
). It has been suggested previously that the slow-growing deep-subsurface strains may be representatives of common ancestors of surface strains such as S. paucimobilis Q1 and S. yanoikuyae B1. Surprisingly, it has been demonstrated for S. paucimobilis Q1 and S. yanoikuyae B1 that the genes encoding the degradation of biphenyl and naphthalene are located on the chromosomal DNA of these strains (Kim et al., 1996
). In accordance with this it was shown in the present study that the plasmids from these strains do not hybridize with the repA probe. This may indicate that in the surface strains the relevant plasmids are lost during or after the transfer of the degradative genes to the bacterial chromosome. However, the results obtained for Sphingomonas sp. EPA505 in the course of the present study, together with those of a previous preliminary communication (Bergeron et al., 1998
), suggest that in surface strains the relevant degradative genes can also be encoded on plasmids.
The hybridization and PCR experiments suggested that plasmids belonging to the same incompatibility group as pNL1 are also present in some strains that have not been described as naphthalene- or biphenyl-degrading organisms. Thus, it was shown that a 240 kb plasmid from the dibenzofuran-degrading strain Sphingomonas sp. HH69 possessed a replication system similar to that of plasmid pNL1. Previous hybridization experiments had detected a gene (dxnA) on the same plasmid that encodes the large subunit of a putative dibenzofuran/dibenzo-p-dioxin dioxygenase (Basta et al., 2004). These results agree with our previous observations following the transfer of a variant of plasmid pNL1 (labelled with a kanamycin-resistance gene) to strain Sphingomonas sp. HH69 and selection for kanamycin resistance in the Sphingomonas sp. HH69 background. In these experiments, substantial rearrangements in the plasmid pattern of strain HH69 were observed. Thus, in all recovered transconjugants, the 240 kb plasmid was missing and the gene hybridizing with the dxnA gene probe was found either on a different plasmid or on the chromosome of the transconjugants (Basta et al., 2004
). This indicated that plasmid pNL1 and the 240 kb plasmid from Sphingomonas sp. HH69 have a similar replication system and therefore cannot coexist in the same cell. This observation also suggested that our hybridization typing gave biologically useful information and, in addition, demonstrated that plasmids similar to pNL1 are not restricted to deep-subsurface locations in the USA, because strain HH69 has been isolated from a soil sample in Germany (Fortnagel et al., 1990
).
The experiments discussed above suggested that plasmids belonging to the same incompatibility group as plasmid pNL1 are also found in Sphingomonas sp. EPA505 and Sphingomonas sp. HH69, but that similar plasmids are only rarely present in other xenobiotic-degrading Sphingomonas strains. Furthermore, this suggests that most of the xenobiotic-degrading strains harboured plasmids that presumably belong to other incompatibility groups. Thus, it was found that the plasmids participating in the degradation of naphthalenesulfonates and dibenzo-p-dioxin in S. xenophaga BN6 and S. wittichii RW1 do not belong to the same replication group as plasmid pNL1. The assumption that plasmids pNL1 and pBN6 belong to different replication groups was also supported by the previous observation that, among the sphingomonads, plasmid pNL1 shows a different host range to that of plasmid pBN6 (Basta et al., 2004). This indicated that plasmid pNL1 is just one (though not necessarily representative) example of a degradative plasmid from a Sphingomonas strain. Thus, it will be necessary to acquire more sequence data about the replication regions in order to obtain a more comprehensive picture about the diversity of Sphingomonas plasmids.
The genes for catabolic pathways are often localized in Sphingomonas strains separately from each other, or, at least, are not organized in coordinately regulated operons. This has been described for the genes involved in the degradation of naphthalene, biphenyl and toluene by S. yanoikuyae B1 and S. aromaticivorans F199 (Cho & Kim, 2001; Romine et al., 1999
; Zylstra & Kim, 1997
), naphthalenesulfonates by S. xenophaga BN6 (Keck, 2000
), dibenzo-p-dioxin by S. wittichii RW1 (Armengaud et al., 1998
),
-hexachlorocyclohexane (lindane) by S. paucimobilis UT26 (Miyauchi et al., 1998
; Nagata et al., 1994
), pentachlorophenol by S. chlorophenolica (Cai & Xun, 2002
) and protocatechuate by S. paucimobilis SYK-6 (Masai et al., 1999
) (for a current review see Pinyakong et al., 2003
). This flexible gene organization (e.g. different combinations of conserved gene clusters) could be one of the mechanisms that allow sphingomonads to adapt quickly and efficiently to novel compounds in the environment. From previous work and from the PCR experiments performed in the course of the present study, it is now becoming clear that, at least in strains that degrade biphenyl, naphthalene and compounds that are converted to intermediates common to the naphthalene and biphenyl pathways (such as dibenzofuran and naphthalenesulfonates), certain conserved gene clusters exist that seem to be part of mobile genetic elements able to change their localization in the genomes of these strains (Fig. 7
). Surprisingly, there is no evident biochemical function of the individual gene clusters. A good example of this is gene cluster 2, which has been sequenced from plasmids pNL1 and pBN6, and is probably also present in S. subterranea, S. stygia, S. aromaticivorans B0695, Sphingomonas sp. HH69 and S. macrogoltabidus. This gene cluster probably consists of two transcriptional units, which are transcribed in opposite directions. The annotation of the gene functions of the larger transcriptional unit suggested that the genes code for the large and small subunit of a ring-hydroxylating dioxygenase, a ferredoxin that presumably participates in electron transfer to a ring-hydroxylating dioxygenase, an extradiol ring-fission dioxygenase, and a 2-hydroxychromene-2-carboxylate isomerase [which is necessary for the degradation of polycyclic aromatic hydrocarbons such as naphthalene and anthracene (Kuhm et al., 1993
; Kim et al., 1997
)]. The enzymes encoded by this transcriptional unit would not be able to synthesize a functional ring-hydroxylating dioxygenase (because of the lack of a ferredoxin reductase), nor convert a standard aromatic compound to a diol (because of the lack of a cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase), nor convert 1,2-dihydroxynaphthalene (or any other dihydroxylated intermediate of a degradative pathway for an aromatic compound) to a utilizable intermediate of the glycolytic pathway or the citric acid cycle (because of the lack of a 2'-hydroxybenzalpyruvate aldolase or a different enzyme releasing an aliphatic intermediate from a monocyclic ring-fission product). There is also no evident function for the conserved (divergently transcribed) xylX gene product, which has been annotated to encode for a subunit of an arylcarboxylic acid dioxygenase (e.g. a benzoate dioxygenase). Furthermore, the genes of cluster 1, consisting of bphB and xylC (genes with homologies to a cis-dihydrodiol dehydrogenase and a benzaldehyde dehydrogenase), and of cluster 3, consisting of nahE, xylL and bphA4 (presumably encoding a 2'-hydroxybenzalpyruvate aldolase, a cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase and a ferredoxin reductase), do not encode any evident functional biochemical reaction sequence. Thus, there is currently an obvious contradiction between the genetic evidence, which suggests a strong selective pressure that stabilizes the composition of the individual gene clusters, and the missing physiological explanation for the existence of these conservative mechanisms. A possible solution for this problem might be an incorrect annotation of the function of the proteins that are encoded by the genes of the conserved gene clusters. Therefore, it will be necessary to functionally express the encoded genes and to experimentally determine the encoded enzymic functions.
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Received 16 February 2005;
accepted 7 March 2005.
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