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Applied and Environmental Microbiology, November 2004, p. 6628-6636, Vol. 70, No. 11
0099-2240/04/$08.00+0 DOI: 10.1128/AEM.70.11.6628-6636.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Department of Entomology, University of Minnesota, St. Paul, Minnesota,1 Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland2
Received 8 April 2004/ Accepted 29 June 2004
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Rickettsia peacockii, an endosymbiont of Dermacentor andersoni, the Rocky Mountain wood tick (28), is of particular interest because it may have played a role in the declining prevalence in the North American Rockies of Rickettsia rickettsii, the etiologic agent of Rocky Mountain spotted fever (RMSF) (9). It has long been known that in the Bitterroot Valley of Montana the absence of RMSF outbreaks correlates with the presence of nonpathogenic spotted fever group rickettsiae (SFGR) (6, 7, 18). R. peacockii, also known as the East Side agent, was first detected in ticks collected from the east side of Montana's Bitterroot Valley with a prevalence of up to 80% (7, 28). In contrast, R. rickettsii is nearly absent in ticks on the east side of the valley (34), and most cases of RMSF occur on the west side of the valley, where prevalence of R. rickettsii in ticks is considerably lower (less than 1% [16]) than that of R. peacockii on the valley's east side. While a low prevalence of R. rickettsii may be due to its pathogenic effects on ticks (27), a high prevalence of R. peacockii in tick ovaries might further interfere with maintenance and transmission of R. rickettsii (7).
Although the genomes of R. rickettsii, Rickettsia sibirica, and Rickettsia conorii (31) have been sequenced, very few DNA sequence data are available for nonpathogenic SFGR that could help define their symbiotic nature on a molecular basis. Several genes have been used to establish rickettsial relationships, principally the 16S rRNA gene, citrate synthase gene (gltA), rickettsial outer membrane protein genes A and B (ompA and ompB, respectively), and gene D (15, 40-42, 44). The latter four genes encode proteins and undergo stabilizing (neutral) selection (14), indicating that they are suitable for taxonomic purposes. The molecular and biological traits that differentiate R. peacockii from R. rickettsii (28, 47) include an inability of the former to make a functional OmpA, which could underlie its endosymbiotic nature and apparent confinement to D. andersoni. Pathogenic R. rickettsii expresses OmpA and polymerizes host cell actin, facilitating its adhesion to host cells, cell-to-cell spread, and replication within mammalian and tick hosts (19, 22, 24). Unlike surface protein genes that rapidly evolve in response to host antibodies (52), Fournier et al. (14, 15) found by calculating the ratio of synonymous and nonsynonymous amino acid substitution rates that the ompA and -B genes undergo neutral selection. Because SFGR are predominantly maintained in nature by transovarial transmission through successive tick generations, their evolution is probably more influenced by tick factors than by those of the mammalian host. In order to gain a better understanding of the biological and evolutionary relationship between R. rickettsii and R. peacockii, we expanded analysis of the R. peacockii ompA gene to include a 3.5-kb region downstream of its tandem repeats (Fig. 1). We also sequenced the promoter region and examined ompA transcription using reverse transcription-PCR (RT-PCR). Our analysis included PCR-amplified ompA sequences from genomic DNA of R. peacockii-infected ticks collected in Colorado and from ticks on the east and west sides of the Bitterroot Valley. We anticipate that the new data presented here will aid in developing methods for the genetic manipulation and transformation of tick symbiotic rickettsiae with the aim of improving their potential for the control of tick-borne pathogens.
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FIG. 1. PCR amplification of the rickettsial ompA gene. The 7,088-bp R. rickettsii R strain ompA sequence (GenBank accession no. M31277) (2) is represented by the solid line, with a numerical nucleotide scale. The protein-encoding portion of the gene is represented by the open rectangle, with the tandem repeat region indicated by vertical bars. Overlapping PCR fragments (primer positions in Table 1) are indicated by lines above the open rectangle. The left- and right-most fragments contain the promoter and transcription terminator regions, respectively. Amplified sequences were assembled into a 4,032-bp composite sequence excluding the primer binding sites at the termini.
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To extract genomic DNA, rickettsiae were recovered (38) and lysed in 300 µl of buffer containing 10 mM Tris-HCl (pH 7.8), 0.5 mM EDTA, 0.5% sodium dodecyl sulfate (SDS), 40 µg of RNase A (Promega, Madison, Wis.)/ml, and 250 µg of proteinase K (Fisher, Pittsburgh, Pa.)/ml at 55°C for 2 to 16 h. Lysates were phenol-chloroform extracted, and DNA was ethanol precipitated and resuspended in nuclease-free H2O (Life Technologies, Rockville, Md.).
Ticks and DNA extraction.
We collected adult female D. andersoni ticks on the north fork of Crestone Creek 4 miles upstream of Crestone, Colo. (200 miles south of Rustic, Colo.) in May 2002. We also obtained adult female D. andersoni ticks collected on the east side (Skalkaho Mountain and Burnt Fork) of the Bitterroot Valley, Ravalli County, Mont., or on the west side (near Como Lake) in May 2003 (we thank Tom Schwan, Rocky Mountain Laboratories, Hamilton, Mont., for providing us with these ticks).
To harvest DNA, ticks were surface disinfected by 5 min of agitation in 0.5% bleach followed by 5 min in 70% ethanol and two rinses in sterile H2O. Ticks were dissected individually in sterile Hanks balanced salt solution, and internal tissues were separated from the integument and transferred to 300 µl of lysis buffer (Puregene; Gentra Systems, Minneapolis, Minn.) with 0.2 µg of proteinase K (Sigma, St. Louis, Mo.)/µl and incubated overnight at 55°C. Recovered DNA was resuspended in nuclease-free H2O.
Strain designations.
The R. peacockii strains that we analyzed, whether they were in culture (i.e., DAE100R isolated from ticks originally collected near Rustic, Colo. [47]) or from field-collected ticks (i.e., Skalkaho Mountain, Mont., or Crestone, Colo.) are designated according to the site or locale where the ticks were originally collected.
Primers and PCR amplification.
The primers that we used are listed in Table 1. Gene positions and primer designations are based on those given for R. rickettsii (2, 15, 36, 39, 41, 42) unless stated otherwise. Lyophilized primers were purchased from Invitrogen (Carlsbad, Calif.) or Integrated DNA Technologies (Coralville, Iowa) and dissolved in TE buffer (10 mM Tris-HCl, 1 mM EDTA; pH 8.0). All PCRs were performed in a RoboCycler thermocycler (Stratagene, La Jolla, Calif.), with 0.5 µg, or less, of template DNA and 2.5 U of Taq polymerase (Promega), unless stated otherwise, in a 50-µl reaction volume. Standard buffer, MgCl2, and deoxynucleoside triphosphate concentrations were as recommended by the enzyme manufacturers.
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TABLE 1. Primers used for PCR amplification and sequencing
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PCR amplification and sequencing of rickettsial ompA.
We used primers designed by Fournier et al. (15) to amplify the 5' and 3' ends of the ompA gene (Table 1). Figure 1 provides a map of the ompA gene, indicating the regions targeted by the primers. We amplified the PCR products for sequencing using Pfu Turbo Hotstart DNA polymerase or cloned Pfu DNA polymerase (Stratagene) at 5 U per reaction mixture of 50 µl. Cycling parameters for the cloned polymerase were 94°C for 45 s followed by 35 cycles of 94°C for 45 s, X°C (X = annealing temperature specified below for each primer pair) for 2 min, and 72°C for 1 min followed by a final 10-min extension step at 72°C. For Turbo Hotstart polymerase, denaturation temperatures were increased to 95°C and lengthened by 15 s, and total cycles were reduced to 30. The 5' end of the ompA gene, including the promoter, was amplified as a 381-bp fragment with primer pair 190-(110) and 190-271 (X = 50°C). A 631-bp fragment overlapping the 532-bp product described above was amplified with primer pair 190-70p and 190-701 (X = 48°C). The 3'-end region of the gene was amplified with primer pairs that produced five overlapping fragments as follows: 818 bp with 190-3588 and 190-4406 (X = 42°C); 850 bp with 190-4388 and 190-5238 (X = 46°C); 888 bp with 190-5125 and 190-6013 (X = 46°C); 891 bp with 190-5917 and 190-6808 (X = 42°C); 399 bp with 190-6585 and 190-6984 (X = 46°C). PCR products were purified by electrophoresis (1% agarose), recovered with QIAquick gel extraction spin columns (QIAGEN, Valencia, Calif.), and directly sequenced in forward and reverse directions two to four times with an ABI 377 automated sequencer (Advanced Genetic Analysis Center, University of Minnesota). Consensus sequences were obtained by alignment using the ClustalX multiple-sequence alignment program (20).
Phylogenetic analysis.
Nucleotide sequences of R. peacockii and R. rickettsii Hlp#2 corresponding to R. rickettsii (R strain) ompA positions 91 to 680 and 3635 to 6789 (2) were joined (the tandem repeat region was excluded) so that 3,764 nucleotides were included in the analysis (15). However, because of a premature stop codon in the 5' prerepeat region of the R. peacockii ompA gene, translated amino acid sequences were not used for phylogenetic analysis (28, 47). The ompA sequences of R. peacockii, R. rickettsii Hlp#2, and other Rickettsia species (Table 2) were manually edited in a word processing file with ClustalX. Alignments were imported into PAUP* 4.0b10 (51) for construction of phylogenetic trees, and distance matrices were determined using Kimura's two-parameter option (21). Relationships were analyzed with neighbor-joining (43) and maximum parsimony (48) methods. Node stability of dendrograms was estimated using bootstrap analysis (12) of values obtained from 1,000 trees generated randomly.
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TABLE 2. GenBank accession numbers of Rickettsia ompA sequences used in the phylogenetic analysis
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RT-PCR assays.
RNA was purified from infected and uninfected tick DAE100 cells with the SV total RNA isolation system (Promega). DNase I-treated RNA samples were stored in H2O at 70°C. RT-PCR amplifications were performed using the Access RT-PCR system (Promega) and temperature profiles recommended by the manufacturer. Transcripts of the ompA, gltA, and 17-kDa antigen genes were amplified with the primers listed in Table 1, electrophoresed through 1.5% agarose gels, and stained with ethidium bromide for visualization by UV illumination.
SDS-PAGE and Western blot analyses.
Rickettsiae were gradient purified by centrifugation (20,000 x g for 40 min at 4°C) through 30% diatrizoate (Hypaque 76; Nycomed Inc., Princeton, N.J.). Rickettsiae were washed in Hank's balanced salt solution and resuspended in 0.5 M Tris-HCl (pH 6.8), and approximate protein concentrations were determined by UV spectrophotometry. Sixty-five micrograms of denatured proteins per well was separated by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) through 7.5% mini-gels and stained with Rapid Coomassie blue (Diversified Biotech, Boston, Mass.). For Western blot analyses, proteins were transferred to an Immobilon-P membrane (Millipore Corporation, Bedford, Mass.) (30) and reacted with mouse monoclonal antibody (MAb) 13-5 to rickettsial OmpA (1) diluted 500-fold in phosphate-buffered saline with 3% bovine serum albumin or hamster polyclonal anti-Rickettsia monacensis serum diluted 300-fold (45). Bound primary antibodies were detected using horseradish peroxidase-conjugated goat anti-mouse or anti-hamster immunoglobulin G diluted 1:1,000 and the 4CN membrane peroxidase system (Kirkegaard & Perry Laboratories, Gaithersburg, Md.).
Double fluorescence staining to assess actin tail formation.
IDE8 tick cells (ATCC CRL-11974) grown to confluency on glass coverslips in 24-well plates were inoculated with dilutions of host cell-free R. rickettsii Hlp#2 or DAE100 cells infected with R. peacockii and incubated in a candle jar at 34°C for 7 days (45). Coverslips were fixed, and rickettsiae were labeled with mouse MAb 13-2 to the rickettsial 120-kDa surface antigen OmpB (1), diluted 1:100, and anti-mouse immunoglobulin G conjugated to fluorescein isothiocyanate (Pierce, Rockford, Ill.), while tick cell F-actin was labeled with rhodamine-conjugated phalloidin (Molecular Probes, Eugene, Oreg.) as described elsewhere (19, 24). Coverslips were mounted on microscope slides in phosphate-buffered saline containing 3% bovine serum albumin, 10% glycerol, and 10% (wt/vol) 1,4-diamino-bicyclo(2,2,2)octane (Sigma) and viewed using a Nikon E400 microscope fitted with dual fluorescence illumination and a Nikon DX1200 digital camera.
Nucleotide sequence accession numbers.
GenBank accession numbers for the rickettsial ompA sequences reported in this paper are as follows: R. peacockii Skalkaho, AY357765 and AY357764; R. peacockii Crestone, AY357766 and AY357763; R. peacockii Rustic, AY319292 and AY319291; R. rickettsii Hlp#2, AY319293 and AY319290. Accession numbers for the partial sequences of the 16S rRNA gene for R. peacockii Crestone and Skalkaho strains are AY360093 and AY360094, respectively; for Hlp#2 the partial 16S rRNA sequence accession number is AY573599. The accession number for partial 17-kDa antigen gene sequences of R. rickettsii strain Hlp#2 is AY189818, and those for R. peacockii Crestone and Skalkaho are AY576905 and AY590153, respectively. The partial gltA sequence accession numbers for R. peacockii strains from Crestone and Skalkaho are AY576904 and AY590152, respectively, and for R. rickettsii strain Hlp#2 it is AY189819.
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TABLE 3. D. andersoni females PCR or RFLP positive for bacteria, Rickettsia, and Francisella species
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FIG. 2. RFLP analysis of the rickettsial ompA gene 532-bp PCR product amplified from purified rickettsiae (DAE100R, Rustic) and D. andersoni tick extracts. PCR products were left uncut (U) or were digested with RsaI (R) or PstI (P). A 100-bp DNA size marker ladder is shown on the left of each panel. (A) R. peacockii strain DaE100R (Rpea) and Crestone tick 5 and 6 extracts (DaC5 and 6). (B) R. peacockii (Rpea) and Montana Bitterroot Valley east side tick extracts (DaEs 6, 8, and 10). (C) R. rickettsii Hlp#2 (HlP#2), R. peacockii (Rpea), and Bitterroot Valley west side tick 9 extract (DaWs9). (D) Bitterroot Valley west side tick 12 extract (DaWs12) and R. peacockii (Rpea).
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DNA and translated sequence comparisons of R. peacockii and R. rickettsii ompA PCR products.
We compared the R. rickettsii R and Hlp#2 ompA sequences to those of R. peacockii DaE100R and tick extracts. Sequences of R. rickettsii Hlp#2 and R. peacockii (all strains) were 99.7 and 98.1% identical to R. rickettsii R and 98.3% identical to each other over the total of 4,032 bp. In order to compare the R. peacockii OmpA protein sequence to those of R. rickettsii R and Hlp#2, we reconstructed the open reading frame by restoring G at bp 403 and removing the insertions at bp 4872 and 5828. The reconstructed R. peacockii OmpA sequence was 95.9 and 96.1% identical to those of R. rickettsii R and Hlp#2, which were 99.5% identical.
Phylogeny of SFGR ompA sequences.
Both the neighbor-joining and maximum parsimony phylogenetic analyses revealed four major branches among the SFGR. Three of these branches, as shown in the unrooted phylogram (Fig. 3), were comprised of R. felis, R. australis, and the IRS3 and IRS4 rickettsiae, demonstrating how divergent their ompA sequences are. The remaining SFGR clustered together on the fourth branch, a direct consequence of their more-conserved ompA sequences (the inset phylogram in the figure is an expanded view of the fourth branch using R. felis as outgroup). Within this cluster, five distinct monophyletic groupings with bootstrap supports of 96% or better were obtained (Fig. 3, inset phylogram). One group contained R. rickettsii R and Hlp#2 and R. peacockii (98% bootstrap support), a second comprised R. rhipicephali, R. aeschlimannii, Bar 29, and R. massilae (100%), while R. japonica, R. hulinii, and R. heilongjiangii clustered together in a third group (100%). R. mongolotimoniae, R. sibirica strain S, R. africae, and R. parkeri formed another group (99%). A fifth group contained R. conorii, the Israeli tick typhus, and the Astrakhan fever rickettsiae (98%). R. montanensis, R. slovaca, and R. honei did not cluster with any other rickettsiae. Maximum parsimony and neighbor-joining analyses using the IRS as the sister outgroup and deleting R. felis and R. australis gave the same groupings with similar bootstrap values (data not shown).
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FIG. 3. Phylogenetic tree (neighbor-joining phylogram) of SFGR (Table 2) inferred from comparison of rickettsial ompA sequences. Numbers are the proportion of 1,000 bootstrap resamplings that supported the topology. Phylograms constructed using maximum parsimony tree-building analyses were similar. The inset phylogram in the figure is an expanded view of the fourth branch, using R. felis as an outgroup. A monophyletic group containing R. peacockii and R. rickettsii is shown in bold.
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Transcriptional regulatory element sequence comparison and RT-PCR assays.
The R. rickettsii R and Hlp#2 promoter sequences were identical, but those from R. peacockii and ticks DaEs1 (Montana) and DaC3 and -8 (Colorado) contained a T-to-C transition at bp 12 and a G-to-T transversion at bp 54 (also present in the R. conorii sequence; GenBank accession no. AE006914). The R. peacockii and tick DNA sequences additionally contained a transversion at bp 61 that altered the putative ribosome binding site from AAGG (as in R. rickettsii ompA) to AAGC. The 140-bp transcription terminator region (bp 6820 to 6960) was identical among all sequences. The minor differences in the core promoter regions of ompA implied that the R. peacockii promoter was functional. Indeed, RT-PCR results obtained with the ompA primer set 190-70p and 190-701 indicated active transcription of ompA mRNA by R. peacockii Rustic (DAE100R). Control RT-PCR assays using RNA from R. rickettsii Hlp#2 and R. peacockii with primers for citrate synthase (gltA) or the 17-kDa antigen likewise yielded the predicted PCR products, whereas reactions lacking reverse transcriptase were negative (Fig. 4).
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FIG. 4. RT-PCR detection of R. peacockii DaE100R and R. rickettsii Hlp#2 ompA, citrate synthase (gltA), and 17-kDa surface antigen gene transcripts. Control reactions were performed on RNA extracts without reverse transcriptase, and PCR-only reactions were performed with DaE100R DNA for comparison of product sizes with those of RT-PCRs. The relative gel migration positions of 400- and 600-bp markers (Life Technologies) are indicated on the left.
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FIG. 5. SDS-PAGE and immunoblot analyses of R. peacockii DaE100R, R. ricketsii Hlp#2, and Rickettsia sp. MOAa proteins. (A) Coomassie blue-stained SDS-PAGE gel. (B) Western blot probed with MAb 13-5 against rickettsial OmpA. (C) Western blot probed with polyclonal sera against R. monacensis to show absence of OmpA but presence of OmpB in R. peacockii DAE100R. Large arrows indicate the position of the 190-kDa OmpA, and arrowheads indicate the position of the 120-kDa OmpB. Small arrows indicate the relative gel migration positions of SeeBlue protein molecular mass markers (Invitrogen).
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We have shown that similar or identical R. peacockii strains are still prevalent in D. andersoni in the original Bitterroot Valley, Mont., location described for the East Side agent (7, 28) and that they also occur in both northern and southern Colorado D. andersoni populations. We propose that R. peacockii is likely to be more geographically widespread than previously believed even though, given its lack of infectivity for amplifying vertebrate hosts, transovarial transmission may alone be responsible for its maintenance in tick populations. The presence of R. peacockii in ticks is believed to influence the transmission dynamics of pathogenic R. rickettsii strains through a mechanism involving competitive exclusion from the tick host (7, 9), and further investigation of the prevalence of R. peacockii in tick populations is warranted given its potential role in the epidemiology of spotted fever.
Several earlier phylogenetic analyses of SFGR utilized sequences from only a portion of ompA, resulting in ambiguous trees that were not well supported by other data, such as biogeography (52). The new analysis presented here is based on the complete ompA gene except the repeats and demonstrates that among the SFGR, the nonvirulent R. peacockii is most closely related to R. rickettsii. This observation provides an opportunity to uncover mechanisms underlying the pathogenesis of R. rickettsii through molecular genetic approaches that would be facilitated by an effort to completely sequence the R. peacockii genome. The phylogenetic comparison further resolved a long-standing ambiguity (33) concerning the relationship of R. rickettsii Hlp#2 to other R. rickettsii strains. Despite the fact that virulent R. rickettsii is associated with Dermacentor ticks and that Hlp#2 was isolated from Haemaphysalis ticks collected from cottontail rabbits, they are clearly more closely related to each other than to any other member of the SFGR. Possible simultaneous circulation of attenuated Hlp#2-like (11, 33) and virulent Rickettsia strains with similar or identical major antigenic epitopes among vertebrates and ticks could be another significant variable in the epidemiology of RMSF.
DNA sequence comparison of the ompA promoter regions of R. peacockii, R. conorii, and R. rickettsii R and Hlp#2 strains demonstrated that they were nearly identical, with appropriately spaced (17 bp) 10 and 35 box consensus sequences, whose functional identity has been validated in the case of strain R by primer extension analysis (36). Curiously, this close identity did not extend to the ompA promoter regions of R. australis (49) and R. felis (5) (GenBank accession nos. AF149108 and AF191026), which have many differences including, respectively, a T-to-A transversion and an A-to-G transversion within the 10 box consensus. In addition, the R. felis sequence contains a 6-bp insertion immediately upstream of the 10 box consensus that results in a suboptimal 23-bp spacer between the 10 box and the 35 box consensus sequence (otherwise identical among all six of the above sequences).
In conclusion, the close relationship of R. peacockii to R. rickettsii was revealed by the high degree of sequence similarity among their ompA genes, supported by our analyses of the 16S rRNA, citrate synthase, and 17-kDa antigen gene sequences. The nearly identical R. peacockii ompA promoter region compared to that of R. rickettsii strain R suggested that it was functional, as confirmed by RT-PCR analysis. However, our sequence data showing a weakened ribosome binding site within the mRNA leader and multiple premature stop codons within the OmpA reading frame implied severely compromised translation. Not surprisingly, no OmpA translation products could be detected in R. peacockii protein extracts. R. peacockii is poorly infectious and exhibits slow growth in tick cells relative to that of Hlp#2 (46). Moreover, double immunolabeling studies failed to demonstrate actin tail structures that were present in the same cell line infected with R. rickettsii Hlp#2. These results support the hypothesis that OmpA, possibly in conjunction with RickA (17), accelerates cell-to-cell spread of rickettsiae. Genetic transformation of R. rickettsii and in vitro cell-free transcription-translation experiments would aid in testing this hypothesis, but no such expression system exists for the obligate intracellular rickettsiae, and rickettsial transformation techniques, including site-directed mutagenesis, are in their infancy (37).
We are grateful to Michael Herron for critical review of the manuscript.
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