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Borrelia burgdorferi: a (somewhat) clonal bacterial species
News & Comment
TRENDS in Microbiology Vol.9 No.10 October 2001
471
the ospC locus have been identified, bacteria with identical ospC genes have been isolated at different points throughout the world1. Other antigen-encoding loci exhibit similar conservation: although there is evidence of historical recombination among erp (ospE–F related) genes8, they appear to be fairly stable in nature. As an example, the erp genes of B. burgdorferi strain 297, which was isolated from the cerebrospinal fluid of a human neuroborreliosis patient in Connecticut, USA, are identical to those of strain Sh-2-82, isolated from a tick collected on Shelter Island, New York, USA (B. Stevenson and J.C. Miller, unpublished). The recent sequencing of a B. burgdorferi genome9,10 has provided evidence of large-scale incorporation of DNA from external sources. Comparisons of G+C content indicate several regions of heterogeneity9. One significant example is the vlsE expression locus and its related silent cassettes. This approximately 10 kb region contains ~50% G+C, whereas most of the bacteria’s genome contains only 21–32% G+C9, suggesting recent incorporation of these sequences from another organism. Although Dykhuizen and Baranton note a similarity between B. burgdorferi vlsE and B. hermsii vmp17, the B. hermsii gene contains only 36.8% G+C (GenBank accession number L04788). There is also no evidence in the B. burgdorferi genome of a second DNA polymerase that could specifically replicate only the vlsE region, as they suggest. Thus, the vlsE locus might well be a recently acquired pathogenicity island. The B. burgdorferi chromosome is not entirely stable. A large region found near one telomere of some strains is frequently absent from other bacteria11. This DNA is occasionally found on plasmids, and these alterations are unrelated to the bacteria’s genovar11. It is not yet known whether the chromosomes of certain bacteria are degenerating, or if DNA has moved into other bacteria (possibly on plasmids) and recombined into the chromosome. It can be concluded that DNA exchange among B. burgdorferi bacteria occurs in nature, but is a rare event1. Most of these DNA exchanges and subsequent recombination events probably involved fairly small DNA fragments, although larger fragments have apparently been incorporated into the genome. As suggested by Dykhuizen and Baranton, the lack of identifiable transposons could be
attributable to the generally small size of incorporated DNA fragments. But one wonders why such parasitic DNAs could not move between bacteria via the cp32-encoded bacteriophages or the gene-transfer agent hypothesized by Dykhuizen and Baranton? Curiously, the genome of B. burgdorferi strain B31 contains several genes bearing similarities to transposases of other bacteria9,10. Although all the strain B31 genes appear to be defective pseudogenes, it is conceivable that other B. burgdorferi contain intact genes. Perhaps B. burgdorferi contains parasitic DNAs after all?
Letters
Borrelia burgdorferi: a (somewhat) clonal bacterial species In their recent review article, Dykhuizen and Baranton1 reviewed the evidence for DNA exchange between Borrelia burgdorferi, most of which I agree with completely. I would, however, like to point out to readers that, although the authors refer to many of the different variants of Lyme disease spirochetes as separate species, not all researchers in the field agree with this divisive system. Genetic variants are probably indicative of different lineages, but there is no evidence that the identified differences are significant enough to warrant the division of Lyme disease spirochetes into multiple species. A growing number of species names have been proposed, based on such criteria as the sequence of a non-coding chromosomal region (the rrfA–rrlB intergenic region) or the presence of certain restriction sites in the chromosome2. Under such definitions, a bacterium could change species as a result of only a few point mutations. Additionally, some genetic loci used for definition of species are known to be exchanged between distantly related bacteria1–4, so an organism can be assigned to two or more ‘species’ depending upon the criterion used4. Most importantly, despite numerous attempts, the various manifestations of Lyme disease in humans cannot be conclusively attributed to infections with specific types of bacteria: different variants have been identified from patients with many similar symptoms2,5–7. For these reasons, it is more appropriate that these genetic variants be called ‘genovars’ of a single species, B. burgdorferi. Viewing all these bacteria as members of a single species, which can encounter each other in the same warm-blooded and arthropod hosts in nature, makes it easy to understand how genetic exchanges can occur. As Dykhuizen and Baranton so well explain, the chromosome and some plasmids of B. burgdorferi are largely clonal, with very little variation among, and between, genovars1. Exceptions to this rule generally consist of genes encoding outer surface proteins, which might be targets for host immune responses and thus be under selective pressure for variation. Yet recombination appears to be rare even among these loci. Although many variants of http://tim.trends.com
Brian Stevenson Dept of Microbiology and Immunology, University of Kentucky College of Medicine, MS415 Chandler Medical Center, Lexington, KY 40536-0298, USA. e-mail: [email protected] References 1 Dykhuizen, D.E. and Baranton, G. (2001) The implications of a low rate of horizontal transfer in Borrelia. Trends Microbiol. 9, 344–350 2 Wang, G. et al. (1999) Molecular typing of Borrelia burgdorferi sensu lato: taxonomic, epidemiological, and clinical implications. Clin. Microbiol. Rev. 12, 633–653 3 Dykhuizen, D.E. et al. (1993) Borrelia burgdorferi is clonal: implications for taxonomy and vaccine development. Proc. Natl. Acad. Sci. U. S. A. 90, 10163–10167 4 Wang, G. et al. (2000) Two distinct ospA genes among Borrelia valaisiana strains. Res. Microbiol. 151, 325–331 5 Eiffert, H. et al. (1995) Nondifferentiation between Lyme disease spirochetes from vector ticks and human cerebrospinal fluid. J. Infect. Dis. 171, 476–479 6 Jaulhac, B. et al. (2000) Direct molecular typing of Borrelia burgdorferi sensu lato species in synovial samples from patients with lyme arthritis. J. Clin. Microbiol. 38, 1895–1900 7 Ryffel, K. et al. (1999) Scored antibody reactivity determined by immunoblotting shows an association between clinical manifestations and presence of Borrelia burgdorferi sensu stricto, B. garinii, B. afzelii, and B. valaisiana in humans. J. Clin. Microbiol. 37, 4086–4092 8 Stevenson, B. et al. (2000) Repetition, conservation, and variation: the multiple cp32 plasmids of Borrelia species. J. Mol. Microbiol. Biotechnol. 2, 411–422 9 Casjens, S. et al. (2000) A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol. Microbiol. 35, 490–516 10 Fraser, C.M. et al. (1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390, 580–586 11 Casjens, S. et al. (1997) Telomeres of the linear chromosomes of Lyme disease spirochaetes: nucleotide sequence and possible exchange with linear plasmid telomeres. Mol. Microbiol. 26, 581–596
0966-842X/01/$ – see front matter © 2001 Elsevier Science Ltd. All rights reserved. PII: S0966-842X(01)02139-4
TRENDS in Microbiology Vol.9 No.10 October 2001
471
the ospC locus have been identified, bacteria with identical ospC genes have been isolated at different points throughout the world1. Other antigen-encoding loci exhibit similar conservation: although there is evidence of historical recombination among erp (ospE–F related) genes8, they appear to be fairly stable in nature. As an example, the erp genes of B. burgdorferi strain 297, which was isolated from the cerebrospinal fluid of a human neuroborreliosis patient in Connecticut, USA, are identical to those of strain Sh-2-82, isolated from a tick collected on Shelter Island, New York, USA (B. Stevenson and J.C. Miller, unpublished). The recent sequencing of a B. burgdorferi genome9,10 has provided evidence of large-scale incorporation of DNA from external sources. Comparisons of G+C content indicate several regions of heterogeneity9. One significant example is the vlsE expression locus and its related silent cassettes. This approximately 10 kb region contains ~50% G+C, whereas most of the bacteria’s genome contains only 21–32% G+C9, suggesting recent incorporation of these sequences from another organism. Although Dykhuizen and Baranton note a similarity between B. burgdorferi vlsE and B. hermsii vmp17, the B. hermsii gene contains only 36.8% G+C (GenBank accession number L04788). There is also no evidence in the B. burgdorferi genome of a second DNA polymerase that could specifically replicate only the vlsE region, as they suggest. Thus, the vlsE locus might well be a recently acquired pathogenicity island. The B. burgdorferi chromosome is not entirely stable. A large region found near one telomere of some strains is frequently absent from other bacteria11. This DNA is occasionally found on plasmids, and these alterations are unrelated to the bacteria’s genovar11. It is not yet known whether the chromosomes of certain bacteria are degenerating, or if DNA has moved into other bacteria (possibly on plasmids) and recombined into the chromosome. It can be concluded that DNA exchange among B. burgdorferi bacteria occurs in nature, but is a rare event1. Most of these DNA exchanges and subsequent recombination events probably involved fairly small DNA fragments, although larger fragments have apparently been incorporated into the genome. As suggested by Dykhuizen and Baranton, the lack of identifiable transposons could be
attributable to the generally small size of incorporated DNA fragments. But one wonders why such parasitic DNAs could not move between bacteria via the cp32-encoded bacteriophages or the gene-transfer agent hypothesized by Dykhuizen and Baranton? Curiously, the genome of B. burgdorferi strain B31 contains several genes bearing similarities to transposases of other bacteria9,10. Although all the strain B31 genes appear to be defective pseudogenes, it is conceivable that other B. burgdorferi contain intact genes. Perhaps B. burgdorferi contains parasitic DNAs after all?
Letters
Borrelia burgdorferi: a (somewhat) clonal bacterial species In their recent review article, Dykhuizen and Baranton1 reviewed the evidence for DNA exchange between Borrelia burgdorferi, most of which I agree with completely. I would, however, like to point out to readers that, although the authors refer to many of the different variants of Lyme disease spirochetes as separate species, not all researchers in the field agree with this divisive system. Genetic variants are probably indicative of different lineages, but there is no evidence that the identified differences are significant enough to warrant the division of Lyme disease spirochetes into multiple species. A growing number of species names have been proposed, based on such criteria as the sequence of a non-coding chromosomal region (the rrfA–rrlB intergenic region) or the presence of certain restriction sites in the chromosome2. Under such definitions, a bacterium could change species as a result of only a few point mutations. Additionally, some genetic loci used for definition of species are known to be exchanged between distantly related bacteria1–4, so an organism can be assigned to two or more ‘species’ depending upon the criterion used4. Most importantly, despite numerous attempts, the various manifestations of Lyme disease in humans cannot be conclusively attributed to infections with specific types of bacteria: different variants have been identified from patients with many similar symptoms2,5–7. For these reasons, it is more appropriate that these genetic variants be called ‘genovars’ of a single species, B. burgdorferi. Viewing all these bacteria as members of a single species, which can encounter each other in the same warm-blooded and arthropod hosts in nature, makes it easy to understand how genetic exchanges can occur. As Dykhuizen and Baranton so well explain, the chromosome and some plasmids of B. burgdorferi are largely clonal, with very little variation among, and between, genovars1. Exceptions to this rule generally consist of genes encoding outer surface proteins, which might be targets for host immune responses and thus be under selective pressure for variation. Yet recombination appears to be rare even among these loci. Although many variants of http://tim.trends.com
Brian Stevenson Dept of Microbiology and Immunology, University of Kentucky College of Medicine, MS415 Chandler Medical Center, Lexington, KY 40536-0298, USA. e-mail: [email protected] References 1 Dykhuizen, D.E. and Baranton, G. (2001) The implications of a low rate of horizontal transfer in Borrelia. Trends Microbiol. 9, 344–350 2 Wang, G. et al. (1999) Molecular typing of Borrelia burgdorferi sensu lato: taxonomic, epidemiological, and clinical implications. Clin. Microbiol. Rev. 12, 633–653 3 Dykhuizen, D.E. et al. (1993) Borrelia burgdorferi is clonal: implications for taxonomy and vaccine development. Proc. Natl. Acad. Sci. U. S. A. 90, 10163–10167 4 Wang, G. et al. (2000) Two distinct ospA genes among Borrelia valaisiana strains. Res. Microbiol. 151, 325–331 5 Eiffert, H. et al. (1995) Nondifferentiation between Lyme disease spirochetes from vector ticks and human cerebrospinal fluid. J. Infect. Dis. 171, 476–479 6 Jaulhac, B. et al. (2000) Direct molecular typing of Borrelia burgdorferi sensu lato species in synovial samples from patients with lyme arthritis. J. Clin. Microbiol. 38, 1895–1900 7 Ryffel, K. et al. (1999) Scored antibody reactivity determined by immunoblotting shows an association between clinical manifestations and presence of Borrelia burgdorferi sensu stricto, B. garinii, B. afzelii, and B. valaisiana in humans. J. Clin. Microbiol. 37, 4086–4092 8 Stevenson, B. et al. (2000) Repetition, conservation, and variation: the multiple cp32 plasmids of Borrelia species. J. Mol. Microbiol. Biotechnol. 2, 411–422 9 Casjens, S. et al. (2000) A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol. Microbiol. 35, 490–516 10 Fraser, C.M. et al. (1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390, 580–586 11 Casjens, S. et al. (1997) Telomeres of the linear chromosomes of Lyme disease spirochaetes: nucleotide sequence and possible exchange with linear plasmid telomeres. Mol. Microbiol. 26, 581–596
0966-842X/01/$ – see front matter © 2001 Elsevier Science Ltd. All rights reserved. PII: S0966-842X(01)02139-4