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Applied and Environmental Microbiology, March 2006, p. 2247-2253, Vol. 72, No. 3
0099-2240/06/$08.00+0 doi:10.1128/AEM.72.3.2247-2253.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
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Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
Received 21 October 2005/ Accepted 12 December 2005
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Studies to investigate what genetic changes had taken place that accompanied this high level of arsenic resistance have been carried out with A. caldus. Highly arsenic-resistant strains of A. caldus have been found to contain an unusual Tn21-like ars operon that is not present in less-resistant strains (6, 23, 24). The 12-kb TnAtcArs is unusual in that the tnpA (transposase) and tnpR (resolvase) genes occur on opposite ends of the transposon, unlike other transposons of the Tn21and Tn3 family, where they form an adjacent unit. These two transposon genes flank a series of genes (arsRCDADA orf7 orf8B) associated with arsenic resistance that are themselves unusual. Genes for an ArsR (negative regulator) (20, 27) and ArsC (arsenate reductase) (10, 11) are followed by a tandem duplication of the genes for ArsD (a second repressor) (28) and ArsA (an ATPase that associates with ArsB and links arsenite export to ATP hydrolysis) (22). These genes are followed by genes encoding ORF7 (an NADH-like oxidoreductase), ORF8 (a cystathione-ß-synthase [CBS] domain-containing protein), and ArsB, the arsenite efflux pump. Deletion of one copy of arsDA readily occurs, but this deletion does not appear to affect resistance when cloned on a multicopy plasmid in Escherichia coli (24). Similarly, the inactivation or deletion of ORF7 and ORF8 did not affect arsenic resistance in E. coli. Some strains of highly arsenic-resistant A. caldus have a second transposon that is identical to TnAtcArs except that it extends from the inverted repeat adjacent to tnpR to orf7, at which point it is truncated. This truncated transposon lacks an arsB but nevertheless confers low-level arsenic resistance when cloned on its own in E. coli (23).
As the dominant iron-oxidizing bacterium (5), it was anticipated that L. ferriphilum strains from commercial arsenopyrite biooxidation tanks would also possess effective arsenic resistance mechanisms. Whereas A. caldus is a
-proteobacterium (9), L. ferriphilum is a member of the nitrospira (12), and we wished to determine whether these two phylogenetically distant but highly arsenic-resistant bacteria isolated from the same biooxidation process would have similar mechanisms for arsenic resistance. More specifically, we wished to determine whether the TnAtcArs transposon found in A. caldus (24) was also present in highly arsenic-resistant strains of L. ferriphilum. We therefore examined the arsenic resistance mechanisms of a strain of L. ferriphilum isolated from a commercial biooxidation tank treating a gold-bearing arsenopyrite concentrate at the Fairview mine (South Africa) and compared these mechanisms with those of other L. ferriphilum isolates.
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(Table 1) cells were transformed with the ligation mix and plated onto Luria agar plus ampicillin (100 µg/ml). Colonies were scraped off and used to prepare the gene bank. The bank was transformed into the E. coli arsenic mutant ACSH50Iq, and transformants able to grow on LB plates containing 0.5 mM arsenite were selected. Twelve arsenic-resistant transformants were isolated, their plasmids were mapped, and all were found to have regions in common. One of these, pLfTnArs, was selected for further analysis. The source of insert DNA was confirmed by Southern hybridization using three different fragments as a probe. Total DNA of L. ferrooxidans Fairview and pLfTnArs digested with various restriction enzyme combinations generated fragments that were the same size as the cloned fragments, indicating that the insert DNA originated from L. ferriphilum Fairview (data not shown). Furthermore, the signals obtained suggested that there were two copies of the transposon present on 10-kb and 12-kb BamHI fragments. L. ferriphilum Fairview genomic DNA was digested with BamHI, and fragments in the 8- to 14-kb size range were used to generate a mini gene bank in the same way as described above. This gene bank was screened in E. coli ACSH50Iq for arsenite resistance to isolate the 10-kb and 12-kb transposon-containing fragments. Restriction mapping confirmed that the two transposons were identical between the invert repeats but differed in the flanking regions, indicating that they occurred in two different locations on the L. ferriphilum genome. |
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TABLE 1. Bacterial strains, plasmids, and primers used in this study
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FIG. 1. Diagrammatic representation of the two ars operons isolated from L. ferriphilum Fairview identified on plasmids pLfTnArs (transposon) (TnLfArs) and pLfArs (chromosome) (Lf ars) and the arrangement of the arsenic transposons identified in Acidithiobacillus caldus (TnAtcArs) (GenBank accession number AY821803) (24), Methylobacillus flagellatus (accession number NZ_AADX01000013), and Alcaligenes faecalis (accession number AY297781). Inverted repeats are shown as vertical black bars. The white box downstream of M. flagellatus arsB represents a 39-aa TnpA remnant (see the text).
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TABLE 2. Comparison of the L. ferriphilum Fairview Ars proteins to those in other organisms
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A BLAST search using the L. ferriphilum ars genes indicated that they were most similar to transposon-related ars genes recently identified in Methylobacillus flagellatus (GenBank accession number NZ_AADX01000013) and Alcaligenes faecalis (accession number AY297781), although studies of these ars transposons have not been reported. A comparison of the operon structures of the four ars transposons identified thus far is shown in Fig. 1. In general, the operon structures of TnLfArs, TnAtcArs, and the Alcaligenes faecalis transposons are most closely related, with TnAtcArs having an additional NADH oxidoreductase-like ORF7 and the Alcaligenes faecalis transposon appearing to have undergone a deletion of tnpR and an inverted repeat. The structure of the M. flagellatus transposon is different in that the tnpA and tnpR genes are adjacent to each other as for most other Tn21 subfamily (and Tn3 family) transposons where they form a functional unit (13). In addition, the M. flagellatus arsR and arsC genes appear to have been fused. Interestingly, the last 39 amino acids of TnpA are repeated downstream of M. flagellatus arsB, reading in the same orientation as arsB (Fig. 1). This remnant could be the link between the arrangement of the tnpR and tnpA genes in the TnAtcArs, TnLfArs, and Alcaligenes faecalis operons compared to the gene layout in the M. flagellatus operon.
A comparison of the sequence identities of all of the ars transposon-associated gene products with those of TnLfArs is made in Table 2. Unexpectedly, although TnLfArs and TnAtcArs originated from bacteria from the same environment, the amino acid sequences of their gene products were not necessarily the most closely related. TnpR of TnLfArs was most related to that of TnAtcArs, while ArsR and ArsC were equally related to both TnAtcArs and the transposon of Alcaligenes faecalis. However, the predicted ArsD, ArsA, ArsB, and TnpA proteins of TnLfArs were much more related to those of the Alcaligenes faecalis and M. flagellatus transposons than to those of TnAtcArs.
At first glance, the finding of two similar ars transposons in the two types of acidophilic bacteria is not surprising, as transposons, and particularly those of the Tn21 family, are very effective at distributing the genes they carry (13). This finding is consistent with the prediction, reported previously by Woese (26), that "cosmopolitan genes," of which arsenic resistance genes are a typical example, are more likely to be a characteristic of particular environments than of particular organismal lineages. If cosmopolitan genes are not restricted to certain lineages, they might be expected to pass between different types of bacteria within an environment that selects for them. It is highly unlikely that the ars transposons have been passed from A. caldus to L. ferriphilum or vice versa in the biooxidation tank environment. The differences in DNA sequences between the genes and the amino acid sequences of their products are far too substantial for them to have arisen in the 10 to 15 years or less since the biooxidation plants began operation and the time of sample collection. This suggests that although the two types of bacteria have arrived at similar solutions to their need for arsenic resistance, they have acquired the ars transposons independently of each other.
Restriction mapping (Fig. 1) and partial sequence analysis of the chromosomal ars genes present on pLfArs revealed three ORFs with sequence identity to arsR, arsC, and arsB genes as found in the L. ferriphilum acid mine drainage isolate whose genome was partially sequenced (25). Surprisingly, in spite of the acid mine drainage sample having originated from California and the Fairview isolate having originated from South Africa, the nucleotide sequences of these ars genes were identical. The arsRC genes are atypical in that they form one continuous open reading frame and seem to be translated as a fusion protein. The predicted amino acid sequences of these gene products and the equivalent proteins of TnLfArs were not highly conserved (Table 2).
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FIG. 2. Arsenic growth assays performed in E. coli ACSH50Iq in the presence of various concentrations of either arsenite or arsenate. Cultures grown overnight were diluted 100-fold into fresh medium and incubated at 37°C for 5 h, and the absorbance at 600 nm was determined. The incubation time used corresponds to the middle of log growth phase of controls under the same conditions. The resistance was expressed as the percentage of the optical density at 600 nm compared with that of the control culture with no added arsenic. Symbols: , pLfArs; , pLfTnArs; , pEcoBlunt. Each data point represents the results of at least two independent experiments. The error bars indicate standard deviations.
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FIG. 3. RT-PCR analysis of L. ferriphilum Fairview chromosomal arsRCB expression. Total mRNA was isolated from E. coli ACSH50Iq (pLfArs) cells induced with 25 µM sodium arsenite. The RT primer used was LfArsBrtR, and it was used in combination with LfArsBrtF in the PCR (Table 1). Lane 1, marker; lane 2, RT-PCR performed on mRNA from E. coli (pLfArs); lane 3, same as lane 2 except that no AMV reverse transcriptase was added to the reaction; lane 4, PCR performed on plasmid DNA (pLfArs) as a control. To detect DNA contamination in the mRNA extracts, reactions were also performed without any AMV reverse transcriptase.
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To further test this, a translational lacZ fusion of the putative promoter region for arsRCB in pLfArs was made, and ß-galactosidase expression was determined in E. coli ACSH50Iq. A region of the ArsR protein that included 344 bp upstream of the ATG start codon was amplified by PCR using the LfArsRLacZF/LfArsRLacZR primer pair (Table 1). The PCR products were digested with BamHI-EcoRI and ligated into the promoterless lacZ reporter gene of pMC1403, resulting in the construct pLfArsRLacZ. Cultures of E. coli ACSH50Iq cells harboring the various constructs grown overnight were diluted 1:200 into fresh medium containing the appropriate antibiotics, sodium arsenate or sodium arsenite (25 µM) when indicated, and 0.4 mM IPTG (isopropyl-ß-D-thiogalactopyranoside) and incubated at 30°C to an optical density at 600 nm of 0.5. The ß-galactosidase activities were measured using a method described previously by Miller (14). Constructs in which ArsRC (ptacLfArsRC) (Table 1) was expressed from a tac promoter as well as ArsR (ptacLfArsR) (with an artificial translational stop codon inserted between ArsR and ArsC) (Table 1) were added in trans. Similar ß-galactosidase activities of approximately 120 units were obtained for the arsR-lacZ construct in the absence or presence of 25 µM arsenate or arsenite, ArsR, and ArsRC (not shown). Taken together with the arsenic growth studies using E. coli, it was concluded that the L. ferriphilum ars genes present on pLfArs were poorly expressed and regulated in both E. coli and L. ferriphilum. One could speculate that this provided the selection pressure for L. ferriphilum Fairview to acquire TnLfArs to enhance its ability to survive in an arsenic-rich environment, like the biooxidation tanks from which it was isolated.
Expression and regulation analyses of the transposon ars genes were not performed, as a similar study was conducted for the closely related TnAtcArs genes identified in A. caldus in which 25 µM arsenate or arsenite resulted in a fourfold induction (24), and both of these transposons conferred similar resistance to arsenic in E. coli (not shown).
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As only the L. ferriphilum strain originally isolated from the Fairview mine had the TnLfArs, we tested whether this strain was more resistant to growth in arsenic than the L. ferriphilum type strain ATCC 49881 and two L. ferrooxidans strains, DSM2705 and ATCC 49879. L. ferriphilum Fairview was capable of growth and iron oxidation in up to 60 mM As(V) as well as As(III) (data not shown). At higher concentrations, it was difficult to keep the arsenic in the solution, and the resistance of this strain may therefore be higher. L. ferriphilum ATCC 49881 and L. ferrooxidans DSM2705 grew up to approximately 40 mM As(V) and As(III), while L. ferrooxidans ATCC 49879 grew up to 30 mM As(III) and 20 mM As(V). Therefore, L. ferriphilum Fairview had maintained its ability to grow in higher concentrations of arsenic than other strains of Leptospirillum even though it had not been exposed to arsenic during 8 to 10 years of subculture in the laboratory.
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FIG. 4. Transposition of TnLfArs in E. coli. (A) Restriction digest of plasmid from a TnLfArs-containing transconjugant (lane 2), pSa (lane 3), and pLfTnpUC1 (lane 4). DNA was digested with BamHI-HindIII and run on a 1% trans-alternating field electrophoresis gel. Lanes 1 and 5, DNA digested with HindIII and BglII, respectively, as molecular weight markers. (B) Southern hybridization of the gel in A probed with arsD.
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Exactly how these transposons may have evolved relative to each other is difficult to determine given this limited set of data. However, the discovery of four arsenic resistance-associated transposons in widely different geographical locations in bacteria that are physiologically and phylogenetically diverse suggests that other related transposons are likely to be found in other arsenic-rich environments. An understanding of the evolutionary development of these transposons awaits their discovery.
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This work was funded by grant Gun2053356 from the National Research Foundation (Pretoria), the University of Stellenbosch, the BHP-Billiton Johannesburg Technology Centre, and EU framework 6 BioMinE project NMP2-CT-2005.
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