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Applied and Environmental Microbiology, August 2003, p. 4575-4582, Vol. 69, No. 8
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.8.4575-4582.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814,1 Pacific Northwest National Laboratory, Richland, Washington 993522
Received 5 May 2003/ Accepted 4 June 2003
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A present genetic engineering goal for D. radiodurans is its development for bioremediation of U.S. Department of Energy (DOE) mixed radioactive environmental waste sites left over from nuclear weapons production during the Cold War (21, 25, 27, 28). These sites contain immense volumes of waste (3 x 106 m3) that include radionuclides, heavy metals, and toxic organic compounds and have contaminated 40 million cubic meters of soil and 4 trillion liters of groundwater since 1946 (1, 21, 25, 27, 28). While there has been significant progress in engineering D. radiodurans for remediation of radioactive DOE waste environments (5, 8, 15), prospective treatment of contaminated sites with engineered D. radiodurans will be limited to temperatures below 39°C, its maximum growth temperature. However, there is a need to develop bioremediating bacteria that are resistant to both radiation and high temperatures because of the existence of thermally insulated contaminated environments where temperatures are elevated by the decay of long-lived radionuclides (e.g., 137Cs and 90Sr) (1). For example, soil columns beneath at least 67 radioactive leaking tanks at DOE's Hanford Site in south-central Washington State have been contaminated and have recorded temperatures as high as 70°C at depths of greater than 18 m (1). Since D. geothermalis and D. murrayi are both radiation resistant and thermophilic, they have become desirable targets for genetic development of bioremediating strains similar to those developed for D. radiodurans (5, 8, 15) but capable of survival and growth at higher temperatures. Given the need to develop bioremediating bacteria for treatment of radioactive high-temperature waste environments, D. geothermalis and D. murrayi were tested for their transformability with the autonomously replicating Escherichia coli-D. radiodurans shuttle plasmid pMD66 (9), which expresses kanamycin (KAN) and tetracycline (TET) resistance in D. radiodurans and additionally expresses ampicillin resistance in E. coli.
pMD66 and its numerous derivatives (9-12) have been used successfully to functionally express cloned genes in D. radiodurans growing under chronic irradiation. Examples include the mer operon of E. coli (5), which encodes Hg(II) resistance and reduction, and the Pseudomonas operon todC1C2BA (15), which encodes partial degradation of toluene. The present work shows that D. geothermalis is capable of expressing Hg(II)-reducing functions cloned in pMD66 at elevated temperatures and under chronic radiation and, like D. radiodurans (14), is naturally capable of reducing a variety of other metal contaminants present in DOE waste sites.
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5 x 106 cells/ml. For solid medium, Bacto Agar (Difco) or Noble agar (Difco) was added to TGY or MM, respectively, to 1.5% (wt/vol). D. radiodurans was grown at 32°C, and D. geothermalis and D. murrayi were grown at 37°C or at higher temperatures as indicated. E. coli was grown in Luria-Bertani medium at 37°C (9). pMD66 (9) (purified from E. coli) encodes ampicillin resistance (Apr), Kmr, and Tetr in E. coli and Kmr and Tetr in D. radiodurans. When pMD66 is prepared from E. coli, the plasmid transforms D. radiodurans with low efficiency (
50 transformants/µg) (9). However, when the same plasmid is purified from D. radiodurans, it transforms wild-type D. radiodurans with efficiencies as high as 106 transformants/µg (9). Plasmid transformation-restriction in D. radiodurans (9), therefore, distinguishes between the sources of plasmids. When purified from E. coli, the plasmid is called pMD66, and when purified from D. radiodurans, it is called pMD68 (9). The situation for a derivative (pMD300) of pMD66 encoding chloramphenicol resistance (Cmr) is analogous (10). pMD300 purified from E. coli encodes Cmr in E. coli and D. radiodurans and when purified from D. radiodurans is called pMD308 (10). Expression of heterologous genes and antibiotic resistance markers cloned into pMD66-type vectors is driven by two different deinococcal constitutive promoters (P1 and P2) (e.g., see Fig. 2A) that are active on autonomous plasmids in D. radiodurans or when integrated into D. radiodurans chromosomes (11, 12). pMD66-type plasmids contain a deinococcal origin of replication (dORI); an E. coli origin of replication (eORI); and resistance genes including aphA (encoding Kmr), bla (encoding Apr), and/or the mer operon (encoding mercury resistance) (3, 5). |
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TABLE 2. Growth characteristics of D. radiodurans and D. geothermalis grown in mma
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FIG.2. Construction and characterization of Hg(II)-resistant-reducing D. geothermalis. (A) pMD727 (5) was transformed into D. geothermalis, giving strain MD865. (B) Southern blot hybridization of EcoRI-digested total DNA from D. geothermalis (wild type, mer negative) and MD865 (D. geothermalis/mer+) with a radiolabeled mer probe. pMD727 contains a unique EcoRI (E) site. Molecular size standards: /HindIII, as in Fig. 1A and B. Wild-type strain abbreviations are as in Fig. 1. (C) Hg(0) volatilization assays at 32 and 40°C for D. geothermalis, D. radiodurans, MD865 and MD735 (D. radiodurans/mer+), and TGY (growth medium, no cells). (D) Growth curves for MD865 and MD735 in TGY plus 50 µM merbromin [Hg(II)] at 50°C.
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Irradiation.
Growth of cells in the presence of chronic irradiation, 50 Gy/h (137Cs Gammacell 40 irradiation unit [Atomic Energy of Canada Limited]), was carried out as described previously (5, 8, 15). For high-level acute irradiation exposures, early-stationary-phase deinococcal cultures (optical density at 600 nm [OD600] of 0.9 corresponds to
108 CFU/ml) were irradiated without change of broth on ice at 10 kGy/h (60Co Gammacell irradiation unit [J. L. Shepard and Associates; Model 109]). For the deinococcal species under investigation, three independent cell cultures and irradiation treatments of the same kind were performed. Following exposure to the indicated doses, cell suspensions were appropriately diluted and assayed for viability by plate assay on rich (TGY) medium (9). Viability data were used to construct survival curves with standard deviations according to conventional formats (9, 24). The effect of chronic exposure to gamma radiation and Hg(II) on the growth of engineered D. geothermalis was determined using TGY agar plates with and without 30 µM merbromin [Hg(II)] (5). Plates were spotted with
105 cells and following plate inoculation were placed into the 137Cs irradiator (50 Gy/h) for incubation at 50°C for 5 days.
DNA isolation and manipulation.
Isolation of plasmid DNA and total DNA from E. coli, D. radiodurans, and D. geothermalis; use of enzymatic reagents; gel electrophoresis; plasmid rescue in E. coli; radiolabeling of DNA; hybridization; washing of blots; and autoradiography were performed as previously described (9-12). For Fig. 1B, D. geothermalis (wild-type) and D. geothermalis/pMD66 total DNA preparations were digested with EcoRI. The blot was double hybridized with a 1.5-kb XbaI genomic recA (D. radiodurans) probe and a 1.5-kb EcoRI-Bpu10I probe of pBR322 that is specific to pMD66.
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FIG.1. Transformation of D. geothermalis with pMD66 and resistance of pMD66-transformed D. geothermalis to acute gamma radiation. (A) D. geothermalis/pMD66. Total DNA from the indicated strains was uncut or digested with PstI before electrophoresis, blotting, and probing of the blot with a whole-plasmid radiolabeled pMD66 probe. Abbreviations: DEIRA, D. radiodurans; DEIGEO, D. geothermalis. (B) The copy number of pMD66 in D. geothermalis/pMD66 is about threefold higher than its chromosomal copy number. (C) Survival of D. geothermalis/pMD66 following acute gamma radiation. Symbols: open squares, D. geothermalis plated on TGY at 37°C; solid triangles, D. geothermalis/pMD66 plated on TGY-KAN at 37°C; solid diamonds, D. radiodurans plated on TGY at 32°C.
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Metal reduction by D. geothermalis.
The native metal reduction capabilities of D. radiodurans have been examined previously (14). The protocols for examining metal reduction by D. geothermalis are essentially identical to those used for D. radiodurans (6, 14, 30, 31) but at higher temperatures. The ability of D. geothermalis to reduce Fe(III) (as Fe-nitrilotriacetic acid [NTA]) was examined in cultures containing 10 mM lactate in basal medium at 45°C. For the experiment with Cr(VI) and U(VI), cultures were incubated in TGY at 40°C.
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TABLE 1. Transformation of pMD66/68 into D. geothermalis, D. radiodurans and E. coli
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Construction and characterization of Hg(II)-resistant D. geothermalis.
The complete E. coli Hg(II) resistance (mer) operon (4.2 kb, encoding six proteins) (3, 5) has previously been functionally expressed in D. radiodurans by using a pMD66 derivative, pMD727 (5) (Fig. 2A). In D. radiodurans, all six mer genes are necessary for reduction of Hg(II) to Hg(0). pMD727 was successfully transformed into D. geothermalis (Fig. 2B), yielding strain MD865. This construction placed the mer genes under the control of a constitutive D. radiodurans promoter (P2, Fig. 2A), and Southern analysis with a radiolabeled probe containing a 1.5-kb EcoRI-BglII fragment from the mer operon showed no significant homology with the D. geothermalis genome (Fig. 2B). Reduction of Hg(II) to volatile elemental Hg(0) by D. geothermalis strain MD865 was examined by testing for mercury volatilization, which causes film darkening (5, 26). Following 14 h of incubation with Hg(II) in a microplate at 32 or 40°C, covered by X-ray film, wild-type D. geothermalis showed modest Hg(0) volatilization. However, strain MD865 (D. geothermalis/mer+) showed substantial Hg(0) volatilization based on film darkening compared to wild-type D. geothermalis at 32 or 40°C (Fig. 2C). MD865 also was resistant to 50 µM Hg(II) during growth at 50°C (Fig. 2D) and displayed luxuriant growth at 50°C in the presence of 50 Gy/h on solid medium containing 30 µM merbromin (data not shown). Wild-type D. geothermalis did not grow in medium containing 30 µM merbromin in the presence or absence of chronic radiation.
Reduction of metals.
D. geothermalis reduced Fe(III)-NTA in the presence of lactate at 30°C (data not shown) and in the presence of lactate or pyruvate at 45°C (Fig. 3A). At 40°C D. geothermalis rapidly reduced Cr(VI) in TGY cultures under both aerobic and anaerobic conditions (Fig. 3B). AQDS (anthraquinone-2,6-disulfonate) is a quinone-containing organic compound that can be utilized as an electron acceptor for respiration and growth by a variety of dissimilatory metal-reducing bacteria (20). As an electron acceptor, AQDS is reduced to the corresponding dihydroquinone (AH2DS) (20). Reduction of U(VI) by D. geothermalis at 40°C occurred only in the presence of AQDS (Fig. 3C). These results are very similar to the reduction capabilities reported for D. radiodurans at lower temperatures (14).
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FIG. 3. Metalloreduction by wild-type D. geothermalis. (A) Fe(III)-NTA reduction coupled to oxidation of organic substrates at 45°C in the absence of oxygen. (B) Cr(VI) reduction in aerobic or anaerobic conditions as measured by loss of Cr(VI) from solution at 40°C. (C) Reduction of U(VI) in the presence or absence of AQDS as measured by loss of U(VI) at 40°C.
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Our data show that plasmid-based transformation systems developed for D. radiodurans (Fig. 1 and 2) can be used to functionally express cloned genes in D. geothermalis at temperatures as high as 50°C (Fig. 2) and in the presence of chronic irradiation. Plasmids introduced into D. geothermalis are also efficiently expressed following exposure to high-level acute irradiation (Fig. 1C), without any apparent plasmid loss or mutagenesis. The differential hybridization results with a chromosome- and a plasmid-derived probe in MD865 (D. geothermalis/pMD66) (Fig. 1B) support the idea that pMD66 exists in multiple copies in D. geothermalis. The survival of D. geothermalis/pMD66 plated on TGY-KAN was indistinguishable from that found for wild-type D. geothermalis on TGY. As in D. radiodurans, this suggests that multiple identical plasmid copies serve as a substrate for efficient repair by homologous recombination (10). Therefore, these studies establish D. geothermalis and D. radiodurans as the only two extremely radiation-resistant vegetative bacteria that are currently amenable to genetic engineering.
The presence of pMD66 in D. geothermalis as a covalently closed circle was confirmed by plasmid rescue in E. coli (Table 1) (12), and restriction enzyme mapping and Southern analysis confirmed its predicted structure and stability in D. geothermalis (Fig. 1A). When total DNA containing pMD66 was purified from D. geothermalis and transformed back into wild-type D. geothermalis, there was only a small increase in the number of transformants over that with pMD66 purified from E. coli. In contrast, there was a large increase in transformation frequency observed in D. radiodurans with pMD66 purified from D. radiodurans or D. geothermalis over that with pMD66 purified from E. coli (Table 1). Therefore, the plasmid transformation capabilities of D. geothermalis appear to be significantly less than those of for D. radiodurans. While the reasons for this difference are unclear, the fact that pMD66 purified from D. geothermalis could be used to transform D. radiodurans at high efficiency, but not D. geothermalis, suggests that transport of DNA into D. geothermalis is inefficient. Wild-type D. murrayi is naturally resistant to KAN and, therefore, was not tested for transformability with pMD66/68. However, D. murrayi is sensitive to chloramphenicol and could be a suitable host for plasmids encoding Cmr, but we found it to be nontransformable with high concentrations of pMD300/308 (10) purified from E. coli or D. radiodurans and did not investigate this species further.
To demonstrate the utility of D. geothermalis for bioremediation purposes, we introduced the highly characterized Hg(II) resistance operon (mer) of E. coli (3) into D. geothermalis on an autonomously replicating D. radiodurans plasmid (Fig. 2A). Ionic Hg(II) is a prevalent contaminant of radioactive DOE waste sites, where the highest concentration level in contaminated areas has been reported as 10 µM (28). When present in D. radiodurans, the mer operon confers Hg(II) resistance and endows cells with the ability to reduce highly toxic Hg(II) to much less toxic elemental Hg(0) (5). Similarly, we show that strain MD865 (D. geothermalis/mer+) is (i) resistant to the bactericidal effects of ionic Hg(II) at concentrations (50 µM; Fig. 2D) well above the highest concentration reported for Hg(II)-contaminated DOE waste sites, (ii) able to reduce toxic Hg(II) to much less toxic elemental and volatile Hg(0) (Fig. 2C), and (iii) able to functionally express the mer operon in highly irradiating environments (50 Gy/h) at temperatures as high as 50°C. It is notable that the mesophilic E. coli Mer proteins (3) were functional in D. geothermalis growing at 50°C. While mechanisms underlying thermophilicity appear to be complex and currently are not well characterized (23), there is some precedent for the interchangeability of genes from mesophiles and thermophiles. For example, the aspartate aminotransferase gene (aspATSs) of the hyperthermophile Sulfolobus solfataricus has been functionally expressed at mesophilic temperatures in E. coli (2). We believe that numerous other metal resistance functions from other bacteria, specific for other metals, could be cloned into D. geothermalis by this approach.
It was recently shown that under strict anaerobic conditions D. radiodurans can reduce Fe(III)-NTA coupled to the oxidation of lactate to CO2 and acetate (14). D. radiodurans could also reduce U(VI) or Tc(VII) in the presence of AQDS and could directly reduce Cr(VI) in both anaerobic and aerobic conditions (14). The enzymatic reduction of multivalent metals and radionuclides can have a major impact on their solubility and, hence, mobility in the environment. Such changes in solubility make microbial metal reduction a suitable process for immobilizing metals and radionuclides within contaminated environments in situ (8, 25). Localized contaminated sediments and soils at DOE sites can have temperature levels that exceed those that can be tolerated by D. radiodurans. We show that the D. geothermalis suite of metal-reducing capabilities appears to be very similar to that reported in detail for D. radiodurans (14) but functional at higher temperatures (Fig. 3).
We are not aware of expression of any cloned genes in D. geothermalis previous to this report. Our demonstration that plasmids developed for D. radiodurans are functional in D. geothermalis strongly supports the idea that bioremediating gene constructs developed for D. radiodurans could be transferred to D. geothermalis. This could yield metabolically proficient, extremely radiation-resistant, and thermophilic bacteria suitable for the treatment of high-temperature mixed radioactive wastes.
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