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J Mol Evol. Author manuscript; available in PMC Feb 16, 2007.
Published in final edited form as:
PMCID: PMC1800823
EMSID: UKMS122

Adaptive Evolution and Recombination of Rickettsia Antigens

Abstract

The genus Rickettsia consists of intracellular bacteria that cause a variety of arthropod vectored human diseases. I have examined the evolutionary processes that are generating variation in antigens that are potential vaccine candidates. The surface proteins rOmpA and rOmpB are subject to intense positive natural selection, causing rapid diversification of their amino acid sequences between species. The positively selected amino acids were mapped and cluster together in regions that may indicate the location of functionally important regions such as epitopes. In contrast to the rOmp antigens, there is no evidence of positive selection on the intracytoplasmic antigen PS120 despite low selective constraints on this gene. All three genes showed evidence of recombination between species, and certain sequences are clear chimeras of two parental sequences. However, recombination has been sufficiently infrequent that the phylogenies of the three genes are similar, although not identical.

Keywords: Rickettsia, rOmpA, rOmpB, PS120, Positive selection, Recombination

Introduction

Rickettsia is a genus of intracellular parasites of animals and plants that are best known as human pathogens. The louse-vectored bacterium Rickettsia prowazekii causes one of the most severe diseases, epidemic typhus, which kills 10–30% of infected patients (Raoult and Roux 1997). Other human rickettsial diseases include Rocky Mountain spotted fever (Rickettsia rickettsii) and Mediterranean spotted fever (Rickettsia conorii), which are both vectored by ticks, and murine typus (Rickettsia typhi), which is flea vectored (Raoult and Roux 1997). There are at least 10 other rickettsial diseases of humans, many of which were only recognized in the last 20 years. The genus also includes insect-vectored plant pathogens (Davis et al. 1998) and vertically transmitted insect pathogens (Werren et al. 1994).

Unusually for intracellular bacteria, Rickettsia are not enclosed in a host-derived cell membrane vacuole, but are in direct contact with the host's cytoplasm. The outer bacterial membrane is covered by a protein layer arranged in a regular crystalline array (Carl et al. 1990; Ching et al. 1990). One of the components of this protein layer is the rickettsial outer membrane protein B (rOmpB; also called the 120-, 133-, or 135-kDa antigen or SPA), which is attached to the membrane at the carboxyl end of the protein by a hydrophobic membrane spanning region followed by a short hydrophilic anchor (Carl et al. 1990). A second protein, rOmpA, is also an outer membrane protein, and is probably another component of the crystalline layer (Anderson et al. 1990).

Crystalline protein layers in bacteria are known to have a diverse range of roles including cell adhesion, surface recognition, and as a protective coat against a broad range of antagonists (e.g., bacteriophage, lytic enzymes, and antibodies (Sleytr and Messner 1983, 1988)). The rOmp proteins have both been implicated in the invasion of host cells (Li and Walker 1998; Uchiyama 2003). They are also both major antigens and are the principal candidates for vaccines against rickettsial infections (Croquet-Valdes et al. 2001). Another rickettsial antigen is the PS120 protein (the gene is referred to as sca4 or Gene D), which is found within the cytoplasm of the bacteria and is not surface exposed (Schuenke and Walker 1994; Uchiyama 1997).

In this study I have assessed the effects of recombination and natural selection in generating diversity in these antigens. Although many antigens evolve rapidly due to selection to escape the acquired immune response of the host, previous studies have concluded that this is not the case for rOmpA (Fournier et al. 1998). I have revisited this question and detected positive selection acting on both ompA and ompB but not PS120. I also found that the rate of recombination between different species of Rickettsia is low.

Methods

Sequence Alignment

All analyses were performed on previously published sequences of ompA, ompB, and PS120 (Table 1). The nucleotide sequences were initially aligned using ClustalW and then adjusted by eye to account for the predicted protein sequence and to avoid interrupting the reading frame. I have sequentially numbered the codons and amino acids in each gene according to the predicted protein sequences from the R. conorii genome (Ogata et al. 2001). The PS120 alignment includes amino acids 12–1020 of a total of 1026. The ompA alignment includes amino acids 953–2013 of a total of 2021. The region of tandem repeats in ompA is not included in the alignment. The ompB alignment includes amino acids 20–1649 of a total of 1655.

Table 1
Rickettsia sequences

Tree Reconstruction

The phylogenetic trees of these genes were reconstructed by maximum likelihood with the program PAUP* v.4.0b8 (Swofford 1998). The model of sequence evolution for each gene was selected by comparing models by likelihood ratio tests using the program Modeltest v.3.6 (Posada and Crandall 1998). The model selected for both ompA and ompB was GTR + G, which accounts for the base frequency, gamma distributed rate heterogeneity across sites, and six different rates for the transitions between the different nucleotides. The phylogeny of PS120 was reconstructed using the TVM + G model, which is identical to GTR + G except that the two types of transitions (A-G and C-T) occur at the same rate. The maximum likelihood topology was reconstructed by a heuristic search using nearest-neighbor interchanges.

Testing for Positively Selected Codons

The ratio of nonsynonymous-to-synonymous nucleotide substitutions (dN/dS ratio) was estimated to infer the selection pressures acting on the three genes. Neutral evolution will produce a dN/dS value of 1, while dN/dS < 1 indicates purifying selection and dN/dS > 1 directional selection. Because the selection pressures vary between different regions of the protein, the value of dN/dS averaged across all sites can be uninformative. Therefore, an approach was taken that allows dN/dS to differ across different codons.

The analysis was performed using a maximum likelihood model of codon substitution along the phylogenies of the genes (Nielsen and Yang 1998; Yang et al. 2000) implemented by the codeml program in the PAML v3.13d package (Yang 1997). The phylogenies used were reconstructed as described above and include all the taxa in Table 1. These phylogenies are available from the author on request. Codons with alignment gaps were included during the analysis of ompA but not ompB or PS120. This was because in the latter two genes including gaps produced problems with convergence during the iteration process (excluding gaps in ompA produced qualitatively very similar results to those presented here). The distribution of the dN/dS ratio (ω) across sites was estimated using different models of codon substitution (Yang et al. 2000). Model M0 (one ratio) assumes that all sites have the same value of ω. M3 (discrete) assumes three different classes of sites with different ω ratios. M7 (beta) allows sites to have 10 different values of ω, calculated from the beta distribution with parameters p and q. The beta distribution is bounded between 0 and 1 and thus constitutes a null model for testing positive selection. M8 (beta + ω) is similar to M7, but with an additional ω category that can exceed 1.

The hypothesis that some amino acid sites are under positive selection can be tested by comparing two nested models with a likelihood ratio test, where these models differ in whether or not they allow some sites to have values of ω greater than one. In this case M7 is compared to M8, and M3 to M0. The former comparison (M7 and M8) is the most stringent test of positive selection (Anisimova et al. 2001), while the latter (M0 vs. M3) is primarily a test of variation of ω between codons. The null distribution of the likelihood ratio test statistic (2Δl, where Δl is the difference between the log-likelihood scores of the two models) can be approximated using the χ2 distribution with the degrees of freedom being the difference in the number of free parameters between the two models (two when comparing M7 and M8 and four when comparing M0 and M3). Analyses of simulated data sets indicate that this test is conservative (Anisimova et al. 2001).

It has recently been noted that the comparison of M7 and M8 may incorrectly detect positive selection if the distribution of ω in M7 does not follow a beta distribution and many sites have ω near to one (Swanson et al. 2003). Therefore, I also conducted a likelihood ratio test comparing model M8 with M8A (Swanson et al. 2003), which is not sensitive to the distribution of ω. The M8A model is identical to M8 except that ω is fixed as ω = 1. The null distribution of this likelihood ratio test statistic can be approximated using the χ2 distribution with 1 degree of freedom (df) (Swanson et al. 2003).

When the likelihood ratio test suggests the presence of sites under positive selection, an empirical Bayes method was used to calculate the posterior probabilities that each site fell into the ω classes (Yang et al. 2000). Sites with high probabilities of belonging to the class with ω > 1 are likely to be under positive selection. The mean ω ratio for each site (Figs. (Figs.11 and and2)2) was calculated as the average of the ω ratios across the all the ω classes from model 8, with the posterior probabilities used as weights.

Fig. 1
The dN/dS (ω) ratio along the ompA gene estimated as the average of the ω ratios across all the ω classes weighted by their posterior probabilities. Amino acid sites are numbered according to the R. conorii genome sequence. Note ...
Fig. 2
The dN/dS (ω) ratio along the ompB gene. For details see the legend to Fig. 1.

Recombination: Incongruence of Gene Trees

Recom bination between genes can be detected by comparing the phylogenetic trees of multiple genes; if different genes have had different evolutionary histories, then recombination has occurred. Three pairs of alignments were produced (ompB + PS120, ompA + PS120, and ompA + ompB), which only included taxa for which sequences were available for both the genes in question. These alignments are therefore subsets of the larger alignments described above. The phylogeny of each alignment was then reconstructed as described above, and its robustness assessed by 1000 nonparametric bootstrap replicates.

I tested whether the phylogenies reconstructed from the two genes in each pair were significantly different using reciprocal SH tests. In all three comparisons, each gene was forced to take the tree topology of the other gene, and the log likelihood calculated. We then tested whether this significantly reduced the likelihood of the topology relative to the maximum likelihood topology using the SH test (Goldman et al. 2000; Shimodaira and Hasegawa 1999), implemented in the program PAUP* v.4.0b8 (Swofford 1998) using the RELL approximation.

Recombination Within Genes

We used three different approaches to detect recombination. The use of multiple methods has been recommended, as analyses of real and simulated data suggest that individual methods sometimes either fail to detect recombination or give false positives (Posada 2002; Posada and Crandall 2001). The methods were selected to reflect a range of different approaches, and because two have been recommended following power analyses (Posada 2002; Posada and Crandall 2001). All these analyses used the same sequence alignments as in the PAML analysis.

The first method was maximum χ2 (Smith 1992). First, alignments were made from all possible triplets of sequences. For each triplet, sites that were monomorphic or contained gaps were discarded. Then, for every pair of sequences in the triplet, a 100-bp window was slid along the alignment in one-nucleotide steps. At each step, the number of variable sites was compared in the left and right halves of the window using a χ2 test. Potential breakpoints correspond to peaks in the values of χ2. All P values were Bonferroni corrected for multiple tests performed on each alignment. This analysis was implemented using the program RDP (Martin and Rybicki 2000).

The second method used was the Reticulate method (Jakobsen and Easteal 1996). First, a matrix is constructed, each cell of which is a pairwise comparison of two phylogenetically informative sites (excluding sites with more than two states). The cells are classed as compatible if a single tree could be constructed from both sites assuming the minimum number of mutations. The test statistic is the Neighbor Similarity Score (NSS), which is the average proportion of times a cell neighbors a cell of the same type (compatible next to compatible or incompatible next to incompatible). The null distribution of this statistic was generated by recalculating the NSS 104 times from datasets where the order of sites had been permuted. This analysis was implemented using the program RDP (Martin and Rybicki 2000).

Finally, recombination can be detected by a decline in linkage disequilibrium between pairs of sites with increasing distance. This is because as the distance between two sites decreases, there will have been fewer recombination events to break down linkage dis-equilibrium. The linkage disequilibrium between pairs of sites was estimated using two different measures, r2 and |D′|, and the correlation with distance was calculated using Pearson's coefficient (Awadalla et al. 1999; Jorde and Bamshad 2000). The significance of the negative correlation was calculated by a Mantel test. The position of the sites was randomized, the statistic recalculated a minimum of 1000 times, and the significance taken as the proportion of times the correlation coefficient was the same as or more negative than the observed value. The permutation test included sites with two segregating alleles and was performed using the program LDhat (McVean et al. 2002). The analysis was then repeated including only those sites at which both alleles occurred at frequencies of >10%. The exclusion of rare alleles is expected to make the test more powerful because common alleles end to be older and therefore are more likely to show evidence of recombination (Awadalla et al. 1999).

Results

Positive Selection on Antigen Genes

The two outer membrane proteins were both found to be subject to positive selection, causing diversification of their protein sequence. The likelihood scores of the different codon substitution models, the model parameters and sites under selection are shown in Tables Tables22 and and3,3, and the results of the likelihood ratio tests in Table 5. In the ompA gene, likelihood ratio tests indicated that models that included positive selection significantly increased the likelihood scores compared to models without positive selection (Table 5). In total it was estimated that 7% of the codons in this gene are positively selected, and this number is likely to be conservative because the ω ratio of the positively selected class was very high (ω = 8), meaning that codons with ω ratios just over 1 will not be included in this category (Table 2). The results from ompB are broadly similar to those for ompA. Again, models that allow positively selected sites have significantly higher likelihoods than those that do not (Table 5). The proportion of positively selected sites (6%) and estimated ω ratio of those sites (ω = 4) are both lower than was the case for ompA (Table 3).

Table 2
Positively selected sites, log-likelihood scores and parameter estimates for the Rickettsia ompA gene
Table 3
Positively selected sites, log-likelihood scores and parameter estimates for the Rickettsia ompB gene
Table 5
Likelihood ratio tests for positive selection

In contrast to the surface antigens, there is no evidence of positive selection acting on the intracytoplasmic antigen PS120. The ω ratio of the PS120 encoding gene is highly heterogeneous across codons (M1 vs M3; Tables Tables44 and and5).5). Furthermore, the comparison of models M7 and M8 suggests that some of the codons are positively selected (Tables (Tables44 and and5).5). However, this is not a robust result because the ω ratio is only slightly greater than 1 (Table 4). This is confirmed as model M8 is not significantly better than M8A, which does not include positively selected sites (Table 5). Therefore, there is no evidence of positive selection acting on PS120. The significant comparison of M7 and M8 probably results from the distribution of ω ratios across codons being a bad fit to the beta distribution combined with a large proportion of codons evolving nearly neutrally (ω = 1 for 35% of sites in model M8A; Table 4). This suggests that there are many regions of this protein subject to few functional constraints.

Table 4
Positively selected sites, likelihood scores and parameter estimates for the PS120 encoding gene

Mapping Sites Under Selection

The distribution of positively selected sites and conserved sites along the ompA and ompB genes is shown in Figs. Figs.11 and and2.2. The location of codons with the strongest statistical support for being positively selected is also shown in Tables Tables22 and and3.3. In the ompA gene it is notable that most of the positively selected codons are found at the 5′ end of the region analyzed. For example, 68% of the codons that had probabilities over 0.5 of being positively selected are found in the first third of this region (data not shown). The positively selected codons were more evenly distributed along ompB than was the case for ompA, although there was a slight tendency for them to be located in the 5′ end of the gene (65% of the codons that had probabilities over 0.5 of being positively selected are found in the first half of the sequence).

Recombination: Incongruence of Gene Trees

The phylogenies of the three genes are broadly congruent, suggesting that recombination between these species of Rickettsia types is rare. This can be clearly seen from inspection of Figs. Figs.33--5,5, which compare the phylogenies of the three genes. There are some differences in the tree topology, but these are not statistically significant in the comparisons of PS120 vs ompA or ompA vs ompB (Table 6). There is, however, evidence of recombination in the comparison of the ompB and PS120 tree topologies (Table 6).

Fig. 3
Phylogenies of ompA and ompB. Percentage bootstrap support is shown by the nodes. The trees only include taxa where sequences of both genes are available from the same strain.
Fig. 5
Phylogenies of ompA and PS120. For details see the legend to Fig. 3.
Table 6
SH tests for conflicting phylogenetic signals between different genes

Recombination Within Genes

The maximum χ2 test detected breakpoints in all three genes. In total there were 2199 significant χ2 peaks (P < 0.01, Bonferroni corrected) in PS120, 1030 in ompB, and 187 in ompA. These totals are summed across all pairwise comparisons, so they do not reflect the number of crossing over events because each actual crossover event will have been detected in multiple comparisons. All three genes contained breakpoints supported by P < 10−10. A particularly clear breakpoint that was detected by the maximum χ2 test (P <10−13) is shown in Fig. 6. In this case, the ompB gene from R. felis is a clear chimera between two other sequences. It is noteworthy that this R. felis sequence is also partly responsible for the conflict between gene trees described above.

Fig. 6
Polymorphic sites in an alignment of the ompB gene from R. felis (F), Rickettsia sp. strain California 2 (C), and R. prowazekii (P; AF123718). Nucleotides ...

Further support for recombination within the alignments comes from the Reticulate test. In all three cases, the NSS was higher than expected (ompB, NSS = 0.83, P = 0.001; PS120, NSS = 0.78, P < 0.0001; ompA, NSS = 0.92, P = 0.01). This indicates that neighboring sites tend to have more similar phylogenetic histories than more distant sites, as expected when there is recombination.

Recombination events within a gene will result in a decline in linkage disequilibrium with increasing genetic distance. This was assessed for all three genes, both based on the entire dataset and using only segregating sites found in more than 10% of the sequences. The exclusion of rare alleles is expected to increase the power of these tests. Although linkage disequilibrium declines with distance in all three genes, there is only consistent statistical support for this relationship in the case of PS120 (Table 7). Furthermore, following the exclusion of rare alleles, the PS120 encoding gene has the most negative correlation coefficients of the three genes (Table 7).

Table 7
Tests for a decline in linkage disequilibrium with distance

Discussion

Positive Selection

Genes that encode antigens commonly have high rates of nonsynonymous substitutions due to selection favoring antigenic escape mutants. Consistent with this pattern, a substantial proportion of the amino acids in rOmpA and rOmpB is positively selected. This selection pressure drives rapid change in the sequence of these proteins and, therefore, will probably generate antigenic diversity within and between these species of Rickettsia. The results of this study contrast with a previous analysis of ompA that estimated the average dN/dS ratio across the whole gene and failed to detect positive selection (Fournier et al. 1998). The reason for this difference is that while some codons in ompA and ompB are positively selected (dN/dS > 1), others are subject to selective constraints (dN/dS < 1), so the average dN/dS ratio is <1.

It is premature to conclude that selection favoring antigenic escape mutants is the cause of positive selection on ompA and ompB. It is possible that long-term infections of vertebrates may not be an important component in the life cycle of many Rickettsia species. Instead, as in most human infections, rickettsemia in other mammals may be short lived. This led Raoult and Roux (1997) to suggest that transmission may often occur between ticks feeding at the same time on a single host. This is particularly likely, as ticks have a tendency to aggregate. If this is the case, transmission may normally occur before an immune response is mounted against the bacteria, lessening the selection for antigenic change. Furthermore, these genes are also expressed in the arthropod vector, and it may be that the arthropod immune system is the primary selection pressure. They also play a role in the bacteria entering vertebrate cells, and this could also potentially expose them to selection.

I also found that positive selection is not a universal feature of rickettsial antigens, as there is no evidence for positive selection on the PS120 antigen. It is unlikely that functional constraints on PS120 are preventing evolutionary change, because many amino acids evolve nearly neutrally in this protein. It is possible that PS120 is a much less important elicitor of the immune response and is, therefore, under less selection for antigenic change. Alternatively, positive selection on the outer membrane proteins may not be a consequence of their antigenicity, but due to some other function not possessed by PS120 (e.g., adhering to host cells).

The positively selected sites in ompA and ompB tend to cluster together, which is similar to the pattern observed in similar analyses of other antigens (e.g., Crewther et al. 1996). It is commonly thought that these clusters reflect regions of the protein detected by the host immune system. For example, in the gp120 gene of HIV, the positively selected sites are concentrated at the same regions as epitopes (Seibert et al. 1995). More directly, mutations in the HIV Gag polyprotein that cause viral escape from cytotoxic T lymphocyte (CTL) recognition occur at positively selected sites (Leslie et al. 2004).

Can the location of positively selected sites in the omp genes predict the location of epitopes? The most comprehensive attempt to locate epitopes in rOmpB from R. conorii failed to find any in amino acids 458–692, but found evidence for five epitopes in the region 708–820 (Li et al. 2003). As shown in Fig. 1, although there are many positively selected sites in the latter region, there are also some in the region that does not contain epitopes. In the future, further information on the location of epitopes from more species, together with the characterization of binding sites and other functional domains, may provide clues as to the causes of positive selection.

In other pathogens it has been suggested that mapping positively selected amino acids within proteins is a useful method of predicting the location of epitopes (Zanotto et al. 1999). This is clearly not the case here, but maps of selection pressures along the gene could still act as a useful guide in the design of vaccines. The most promising regions of the protein to use as a vaccine will be epitopes in the most strongly conserved regions, as these will be the least variable in natural populations and the least likely to lead to the appearance of antigenic escape mutants.

Recombination

Recombination has profound implications for the evolution of pathogenic organisms. For example, it will lead to the accelerated rates of adaptive evolution, which may result in the spread of alleles resistant to drugs or vaccines. Even extremely rare recombination events can be of great importance in creating mosaic progenitors of successful lineages. Recombination can also complicate the naming and classification of organisms if there is genetic exchange between different “species.” In this case the evolutionary history of species may not follow a simple branching phylogenetic tree but, rather, a more complicated network where each species can have multiple ancestors (Smith et al. 1999).

The genome of R. prowazekii is very unusual among bacterial pathogens in that it contains no “alien genes” acquired from phylogenetically distant species (Karlin 2001). This suggests that the rate of genetic exchange in this genus may be unusually low. However, the genome sequences of R. prowazekii and R. conorii contain several genes involved in homologous recombination (Andersson et al. 1998; Ogata et al. 2001), suggesting that recombination can occur. Furthermore, homologous recombination between two strains of R. prowazekii has been observed in the laboratory (Rachek et al. 1998).

We found clear evidence that recombination has occurred between different species of Rickettsia bacteria. This recombination can be viewed as occurring at an intermediate taxonomic scale to the previous work described above, which looked for genetic exchange between either distantly related taxa (Karlin 2001) or closely related strains of the same species (Andersson et al. 1998; Ogata et al. 2001). Such recombination therefore needs to be considered as a factor during the emergence of new rickettsial diseases or during the spread of drug or vaccine resistance.

I did not attempt to estimate the rate at which recombination is occurring. However, the phylogenies of the three genes, although not identical, were broadly similar. This suggests that the majority of nucleotides in the genome share a common phylogenetic history. There were, however, significant differences in the phylogenetic trees inferred from two of the genes. This may not reflect the exchange of entire genes between bacterial lineages, as one of the key sequences underlying the conflict was itself a recombinant (Fig. 6) Such recombinant sequences can result in the recovery of trees that do not reflect the true phylogeny of either parental sequence (David and Keith 2002).

Fig. 4
Phylogenies of PS120 and ompB. For details see the legend to Fig. 3.

Acknowledgments

This work was funded by a Wellcome Trust Research Career Development Fellowship.

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