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Infection and Immunity, September 2002, p. 4798-4804, Vol. 70, No. 9
0019-9567/02/$04.00+0 DOI: 10.1128/IAI.70.9.4798-4804.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Graduate School of Biomedical Sciences,1 Departments of Pathology and Laboratory Medicine,2 Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, Texas 77225-0708,3 National Institute of Infectious Diseases, Tokyo, Japan4
Received 14 March 2002/ Returned for modification 11 April 2002/ Accepted 23 May 2002
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Efforts to identify virulence-associated genes in B. burgdorferi have been hampered by the lack of efficient methods for genetic manipulation of this bacterium. In recent years, great strides have been made in the development of genetic tools. Initial success in transformation and genetic exchange in B. burgdorferi was achieved by the electroporation of DNA segments containing gyrB with point mutations that conferred resistance to coumermycin (20). Unfortunately, the high rate of recombination into the native gyrB site on the chromosome and the occurrence of natural resistance resulted in a low efficiency when this approach was applied to targeted gene disruption (24). Two additional selectable markers have been developed that circumvent this problem: (i) a kanamycin resistance gene from the Tn903 transposon coupled with either the B. burgdorferi flaB or flgA promoter (2) and (ii) the ermC gene, originally isolated from Lactococcus lactis, which confers resistance to erythromycin (21). These selectable markers have been used to develop both shuttle and suicide vectors that can be used in B. burgdorferi (2, 21, 23). The shuttle vector pBSV2, constructed by Stewart et al. (23), contains the origin of replication and associated genes from cp9 and the ColE1 origin of replication, thus permitting replication in both B. burgdorferi and E. coli. A second shuttle vector, pCE310, which uses the minimal plasmid replication locus from cp32-3, was developed recently by Eggers et al. (5). Transformation with either of these constructs correlated with the loss of the corresponding native plasmid (i.e., cp9 for pBSV2 and cp32-3 for pCE310). The broad-host-range plasmid pGK12 (21) can also be transformed into B. burgdorferi but does not appear to be as stable as the shuttle plasmids containing Borrelia plasmid replication loci (21, 23). Telomere sequences from lp17 inserted into a suicide vector also promote truncation of lp17 at the site of integration, providing another means of genetic manipulation (4). Hübner et al. (8) recently utilized both the erythromycin and kanamycin resistance markers to first disrupt the sigma factor gene rpoN and then restore rpoN expression through a second recombination event. In this manner, they were able to demonstrate the role of RpoN and RpoS in regulation of outer surface protein C (OspC) and decorin-binding protein A (DbpA) expression. Similarly, Sartakova et al. (22) used the same resistance markers to first disrupt the flagellar core protein gene flaB and then complement the mutation, thereby restoring cellular motility. In an effort to increase transformation efficiency, Elias et al. (6) examined a number of transformation parameters and determined that B. burgdorferi low-passage clones were heterogeneous with regard to their transformation efficiencies. Electroporation and a chemical transformation procedure with organisms treated with polyethylene glycol and dimethyl sulfoxide yielded similar transformation frequencies; due to the higher survival rate in the chemical transformation method, a lower number of cells was needed per transformation for this technique (6).
Most B. burgdorferi transformation studies reported to date were performed in high-passage strains that were no longer infectious, and thus far no fully infectious transformants of low-passage strains have been reported. Utilizing pBSV2, Stewart et al. (23) determined that the transformation efficiency of low-passage isolates of B. burgdorferi N40 is at least 70 times lower than high-passage isolates (<5 transformants per µg of DNA compared to 350 transformants per µg of DNA, respectively); the infectivity of the low-passage transformants was not reported. More recently, Elias et al. published a detailed analysis of the infectious isolate B. burgdorferi B31 MedImmune (B31 MI) that included transformation studies. These authors reported transformation and targeted inactivation of the oppAII, rpoS, and chbC genes of low-passage isolates at a very low frequency (<1 transformant per µg of DNA). They were unable to recover any transformants after needle inoculation of mice, although the mice infected with the chbC mutant exhibited an antibody response against the protein P39, indicating at least transient infection. Hübner et al. (8) inactivated and then complemented rpoN in low-passage B. burgdorferi 297 but were also unable to obtain transformants that retained the ability to infect mice. In a separate study, Eggers et al. (5) were not able to transform B. burgdorferi B31 MI with the shuttle vector pCE310 but did isolate transformants of low-passage, infectious B. burgdorferi 297. The efficiency of transformation of low-passage 297, however, was much lower than in high-passage isolates; the infectivity of the transformants was not reported (5). The reasons for this difference in transformation efficiency and for the inability to date to recover fully infectious transformants have not been determined.
In the present study, we investigated the role of plasmid content in the transformation efficiency of a set of high-passage and low-passage clones of B. burgdorferi B31 in which the plasmid profiles had been determined (17). We reasoned that transformability of B. burgdorferi may be related to the absence of certain plasmids, inasmuch as transformation occurs at a higher rate in high-passage strains in which a number of plasmids have been lost (23).
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TABLE 1. Plasmid profiles of B. burgdorferi B31 clones used in this study
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109 in 50 µl) were transformed with 1 to 1.5 µg of plasmid DNA. After electroporation, bacterial cells were immediately resuspended in 1 ml of prewarmed (34°C) BSK-II liquid medium (1) and incubated for 20 to 24 h at 34°C. The cultures were then plated in a soft agar overlay (14) on BSK-II plates with or without kanamycin (0.2 mg/ml) and incubated at 34°C for 2 to 4 weeks. Colony counts were used to determine the transformation efficiency for each clone (transformants/microgram of DNA). Detection of positive transformants. PCR to detect the pBSV2 was performed by using the Amresco Tbr polymerase kit according to the manufacturer's conditions (Euclid, Ohio). Borrelia plasmid DNA was purified by using the Wizard MiniPrep SV kit and genomic DNA was isolated by using the Wizard Genomic DNA Purification Kit (Promega, Madison, Wis.). One microliter of either DNA preparation was used as a template. PCR primers 4795 (5'-GGGAAAACAGCATTCCAGGTATTAGAAG-3') and 4796 (5'-CAGTTCCATAGGATGGCAAGATCC-3') (Integrated DNA Technologies, Coralville, Iowa), which amplify a region of the kanamycin resistance cassette of the shuttle plasmid, were used at a final concentration of 1.25 µM. Reaction solutions were overlaid with 20 µl of ChillOut wax (MJ Research, Cambridge, Mass.), and PCR performed in an MJ Research Minicycler. An annealing temperature of 55°C and 35 cycles were used. Ten-microliter samples of each reaction were electrophoresed in 1% agarose gels and visualized by ethidium bromide staining.
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TABLE 2. Efficiency of transformation of B. burgdorferi B31 clones with pBSV2a
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TABLE 3. Loss of lp25 and lp56 in pBSV2 transformantsa
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28 days after inoculation, or
18 days later than resistant colonies in B. burgdorferi cultures exhibiting high or intermediate transformation rates. The recovered clones from 5A4, 5A8, and 5A15 retained both lp25 and lp56. However, pBSV2 was not detectable in these clones by agarose gel electrophoresis and ethidium bromide staining (data not shown). Furthermore, PCR amplification of the kan gene of pBSV2 with genomic DNA from these clones as a template also yielded negative results (data not shown), indicating that pBSV2 did not integrate into the genome. Therefore, these kanamycin-resistant clones were not a result of transformation by pBSV2 but appear to arise from spontaneous mutations leading to resistance. The lack of detectable pBSV2 transformation of 5A4, 5A8, and 5A15 supports the hypothesis from our transformation efficiency results that lp25 and lp56 play important roles in inhibiting transformation with pBSV2. |
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50-fold, whereas the presence of both completely inhibited transformation. Conversely, B. burgdorferi clones that lacked both lp25 and lp56 had extremely high transformation rates, exceeding 1,000 transformants per µg of DNA. In addition, we were unable to recover transformants from any B. burgdorferi B31 clone that retained lp25. The presence of this plasmid has been shown previously to correlate closely with infectivity in mice (11, 17, 27); therefore, lp25 appears to be required for infectivity in mammals and yet presents a formidable barrier to transformation. Thus, it is likely that the transformation rate in infectious strains is undetectable or exceedingly low because of the presence of lp25; similarly, the loss of full infectivity in those low-passage transformants that are recovered most likely corresponds to the loss of lp25. Kanamycin-resistant colonies in lp25+ lp56+ low-transformation phenotype clones did not contain pBSV2 (Table 3) and apparently resulted from naturally occurring mutations; this result underscores the need to distinguish between "true" transformants and mutants in transformation analyses. With regard to the intermediate transformation phenotype, our working model is that transformation can only occur in the limited number of bacteria that have spontaneously lost lp25. As a result, none of the pBSV2+ transformants recovered from clones of this phenotype that had lp25 prior to electroporation contained detectable lp25. There does not appear to be such a stringent requirement for loss of lp56, in that some transformants obtained from lp25- lp56+ clones still contained lp56 (Table 3). Previous studies demonstrated the recalcitrance of infectious B. burgdorferi strains to transformation and provide additional insight into the possible mechanisms (5, 6, 8). Eggers et al. (5) were also unable to isolate transformants of low-passage B31 MI. When the high-passage isolate B31-UM or the low-passage, infectious 297 strain were utilized, all of the pCE310 transformants examined for plasmid content appeared to lack lp25; lp56 was also absent from the transformants of B31-UM, but this parameter was not reported for the 297 transformants. Clone B31-F had a 50-fold greater transformation efficiency in comparison with B31-UM (5); we speculate that this difference may reflect the presence of lp56 in B31-UM prior to transformation. Hübner et al. (8) obtained disruption mutants of rpoN and rpoS in infectious 297 by using nonreplicating "suicide" vectors. Similarly, Elias et al. (6) were able to isolate targeted disruption mutants of the oppAII, rpoS, and chbC genes from B31 MI utilizing electroporation with suicide plasmid constructs. Thus, transformation with linear constructs or nonreplicating plasmids that must undergo recombination into host replicons to confer antibiotic resistance may be more "permissive" than transformation with an episomal plasmid. Fully infectious organisms were not recovered in either of these studies (6, 8); antibodies against P39 were expressed in mice inoculated with the chbC disruption mutant, a finding consistent with transient infection (6). Attempts by Hübner et al. (8) to restore the infectivity of an rpoN mutant by complementation with a plasmid expressing rpoN were not successful. The decreased infectivity of these disruption mutants could be due to the inactivation of the targeted gene (and insufficient complementation) or, alternatively, to effects secondary to other genetic changes.
DNA restriction or modification systems of other bacteria present barriers to transformation through the restriction site cleavage of unmodified "foreign" DNA. Although data consistent with Dam methylation of DNA in some B. burgdorferi strains has been reported (9), no restriction or modification systems have been characterized.
Analysis of the sequences of lp25 and lp56 (7) reveals that both plasmids encode putative proteins that potentially have both restriction and modification activities (Table 4). Hypothetical protein open reading frames (ORFs) on B. burgdorferi plasmids have been given a designation consisting of the BB prefix, a letter corresponding to the plasmid, and a number indicating the rank order of the ORF on the plasmid (e.g., BBE02) (7). BBE02 on lp25 encodes a putative 1,277-amino-acid (aa) protein that shares a low degree of overall homology and several sequence motifs with the Eco57I type IV restriction-modification system of Escherichia coli (10), LlaGI of Lactococcus lactis (12), and HaeIII of Haemophilus aegypticus (16) (Table 4), as well as with putative methylation proteins from C. jejuni (e.g., ORF Cjo690c) (15) and Halobacterium sp. (VNG6135c) (13). The Eco57I system is the best characterized of this group and is composed of two proteins, M.Eco57I, a methyltransferase, and R.Eco57I, a protein that possesses both methylation and restriction enzyme properties. Rimseliene and Janulaitis (18) recently demonstrated that the catalytic domain 77PDX13EAK of R.Eco57I is required for endonuclease activity, in that site-directed mutagenesis of either 78D or 92E reduced target DNA cleavage to undetectable levels. R.Eco57I also possesses methylase activity and contains a series of methyltransferase signature sequences (Table 4) that are conserved among m6A and m6C DNA methyltransferases (10, 25). LlaGI and HaeIII also have both restriction endonuclease and methylation activities and share the same set of sequence motifs (Table 4). The predicted amino acid sequence of BBE02 has a potential endonuclease catalytic-Mg2+ binding motif (PDX14EFK) at aa 251 to 269 and also contains all four methyltransferase sequences (Table 4). Thus, BBE02 may encode an endonuclease with methylase activity, similar to R.Eco57I.
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TABLE 4. Presence of predicted catalytic-Mg2+-binding domain and methyltransferase signature sequences in B. burgdorferi plasmid-encoded ORFs and comparison with enzymes of other bacteria with both endonuclease and methylase activitiesa
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BBH09, located on lp28-3, encodes a hypothetical protein that shares 92% similarity to the protein product of BBE02, is approximately the same size and contains the same sequences in each of the catalytic and methylation motifs (except for CMII, in which there are 2 aa differences) (Table 4). It should be noted, however, that the pIs of these homologs are quite different (Table 4), which may affect their activities. As with BBE02 and BBQ67, it is not yet known whether BBH09 produces a functional product. However, the only clones in our study that were missing lp28-3 were the high-passage clones HP-J and B31-A, which had high and intermediate transformation efficiencies, respectively (Table 2). All of low-passage clones we tested had lp28-3, and yet these clones exhibit a spectrum of high-, intermediate-, and low-transformation phenotypes. The fact that clones 5A10 and 5A14 exhibited high-transformation rates (Table 2) indicates that the presence of lp28-3 (and hence BBH09) does not interfere greatly with transformation of B. burgdorferi. Other highly speculative possibilities are that the restriction site recognized by BBH09 is modified in the E. coli strain used to prepare pBSV2 in these studies or that pBSV2 lacks this putative restriction site.
The plasmids of B. burgdorferi have undergone extensive duplication and rearrangement events, resulting in numerous paralogous genes and gene fragments (3, 7). BBE02 and BBH09 are members of gbb family 1, which also includes the truncated ORF BBK10 (lp36) and the pseudogenes BBK02.1, BBK25.1 (lp36), BB0849.2 (chromosome), and BBH11.1 (lp28-3). The latter sequences appear to represent inactive segments of an ancestral gene related to BBE02 and contain several frameshifts that resulted in the formation of smaller ORFs; these include ORFs BBK02, BBK03, BBK04, BBK10, BBK28, BBK29, BBK30, and BBO851 (3, 7; http://www.tigr.org). BBQ67 is a member of gbb family 102, which also contains paralogs on lp28-2 (BBG02) and lp28-3 (BBH36.2) and at the opposite end of lp25 from BBE02 (BBE29.1). Within these two paralogous families, only BBE02, BBH09, and BBQ67 appear to encode full-length products that are potentially expressed; all other paralogs appear to be nonexpressed gene fragments resulting from extensive duplication and subsequent decay of DNA segments, as commonly occurs in B. burgdorferi plasmids (3, 7; http://www.tigr.org).
Donahue et al. (4a) have shown that cell extracts (CFE) of H. pylori have the ability to methylate DNA in vitro. Incubation of plasmid DNA with H. pylori CFE in the presence of S-adenosyl-L-methionine protected the DNA from digestion by NlaIII and HaeIII. Also, the treatment of shuttle plasmids with CFE greatly increased the transformation efficiency in H. pylori (4a). Preliminary attempts to use CFE of B. burgdorferi containing lp25 and lp56 have been inconclusive due to nonspecific endonuclease activity present in the B. burgdorferi CFE that completely digests the target DNA (H. Kawabata, unpublished data). Studies to detect restriction and methylation activity in B. burgdorferi are ongoing.
In summary, lp25 and lp56 appear to represent barriers against the transformation of B. burgdorferi. Sequence analyses further indicate that BBE02 and BBQ67 may encode restriction and/or modification enzymes that interfere with the transformation of B. burgdorferi with "unmodified" DNA. Replicons such as the pBSV2 plasmid used in this study would be particularly susceptible to this effect. Introduction of a double-stranded break into an autonomously replicating plasmid would prevent replication and persistence in the cell; however, suicide vectors or linear DNA fragments could potentially recombine with the target sequence even if fragmentation occurs.
It is important to recognize that other possible mechanisms exist. For example, it is possible that the low transformation rate of pBSV2 in lp25+ or lp56+ clones represents a form of plasmid incompatibility, in which the cp9 origin of this construct must "compete" with lp25 and lp56 for plasmid-specific replication or partitioning proteins. cp9, lp25, and lp56 coexist in B. burgdorferi isolates, arguing against a possible incompatibility between the replication loci of these plasmids. In addition, previous studies indicate that antibiotic selection of pBSV2- or pCE310-containing clones favors the loss of the corresponding native plasmids (cp9 and cp32-3, respectively) without affecting the replication of other plasmids (5, 23). Another possible mechanism is that proteins encoded by lp25 and lp56 may alter the surface properties of B. burgdorferi and hence impede the uptake of DNA. Additional analyses are therefore necessary to determine the mechanisms associated with reduced transformation rates in B. burgdorferi strains containing lp25 and lp56. It is anticipated that the identification of lp25 and lp56 as apparent barriers to transformation will help define efficient methods for genetically altering infectious strains of Lyme disease borrelia and hence aid in the identification of important virulence determinants.
This work was supported by National Institutes of Health grant AI37277 from the Institute for Allergy and Infectious Diseases (S.J.N.), Texas Advanced Technology Program grant 011618-0236-1999 (S.J.N.), and grant HS-154 from the Japan Health Sciences Foundation (H.K.).
M.B.L. and H.K. contributed equally to this study.
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