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Suggested role for G4 DNA in recombinational switching at the antigenic variation locus of the Lyme disease spirochete.

Walia R, Chaconas G - PLoS ONE (2013)

Bottom Line: In the work presented here we show that G4 DNA can be formed by sequences within the B31 vlsE locus, prompting us to investigate the presence of potential G4-forming DNA throughout the vls locus of several Lyme spirochete strains and species.We found that runs of G, three nucleotides and longer occur at a very high density, with a greater than 100-fold strand-specific distribution in the vls locus of three B. burgdorferi strains as well as in B. afzelii and B. garinii, in spite of the bias for the use of A-T rich codons in Borrelia species.Our findings suggest the possibility that G4 DNA may be a mediator of recombinational switching at the vlsE locus in the Lyme spirochetes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry & Molecular Biology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada.

ABSTRACT
Antigenic variation through targeted DNA rearrangements provides a powerful diversity generating mechanism that allows a variety of pathogens to stay one step ahead of acquired immunity in their hosts. The Lyme disease spirochete encodes such a system that is required for persistent infection. The vls locus, carried on a 29 kb linear plasmid (lp28-1) in the type strain B31, carries 15 silent cassettes from which information is unidirectionally transferred into the expression locus, vlsE. Recent studies have surprisingly shown that, with the exception of the RuvAB branch migrase, no other known recombination/repair proteins appear to play a role in the recombinational switching process. In the work presented here we show that G4 DNA can be formed by sequences within the B31 vlsE locus, prompting us to investigate the presence of potential G4-forming DNA throughout the vls locus of several Lyme spirochete strains and species. We found that runs of G, three nucleotides and longer occur at a very high density, with a greater than 100-fold strand-specific distribution in the vls locus of three B. burgdorferi strains as well as in B. afzelii and B. garinii, in spite of the bias for the use of A-T rich codons in Borrelia species. Our findings suggest the possibility that G4 DNA may be a mediator of recombinational switching at the vlsE locus in the Lyme spirochetes.

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Distribution of G3–5 runs on the linear plasmids carrying the vls loci in B. burgdorferi strains B31, N40 and JD1.G runs of 3–5 nucleotides in length were counted in the sequence of lp28-1 (Accession NC_001851 and FJ472338) from B31 [8], [52], [53], lp36 (Accession CP002230) from N40 and lp28-1 (Accession NC_017404) of JD1 [36]. The distribution of G3–5 runs on both strands of vls and non-vls DNA was plotted. The coding strand is defined as the strand in which the silent cassettes code for the VlsE protein. The vls DNA includes only the silent cassettes, as the vlsE sequence is only known for B31.
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pone-0057792-g007: Distribution of G3–5 runs on the linear plasmids carrying the vls loci in B. burgdorferi strains B31, N40 and JD1.G runs of 3–5 nucleotides in length were counted in the sequence of lp28-1 (Accession NC_001851 and FJ472338) from B31 [8], [52], [53], lp36 (Accession CP002230) from N40 and lp28-1 (Accession NC_017404) of JD1 [36]. The distribution of G3–5 runs on both strands of vls and non-vls DNA was plotted. The coding strand is defined as the strand in which the silent cassettes code for the VlsE protein. The vls DNA includes only the silent cassettes, as the vlsE sequence is only known for B31.

Mentions: G-runs are not present in the DR’s of other Lyme spirochetes and the DR’s are not believed to be involved in antigenic switching at vlsE (see Discussion). However, their ability to confer unusual properties upon the B31 vlsE locus in vitro, presumably through the formation of G4 DNA, prompted us to investigate the potential for formation of G4 DNA throughout the vls locus in several Lyme spirochetes. We analyzed the sequence of the linear plasmids carrying the vls locus from B. burgdorferi B31, N40 and JD1 [8], [36] for runs of G that were three or longer. These three strains show similar levels of divergence from one another with about 65% identity between vls cassettes [37] and contain clearly different DR’s within the silent cassettes [38]. Analysis of the B31 plasmid lp28-1, which carries the vls locus (Fig. 7), showed the presence of 2–3 G-runs per 1000 bp on either strand in the first 19,000 bp at the left end of the plasmid. In dramatic contrast, the vls region itself (8,239 bp) contained a total of 225 G-runs on the coding strand (27 runs per kb) and only one on the non-coding strand. This grossly unequal weighting of G-runs on the vls coding strand was also apparent on lp36 in strain N40 and on lp28-1 in strain JD1 (Fig. 7). Moreover, the somewhat more divergent vls regions from B. garinii Ip90 and B. afzelii ACA1 [38] also displayed 26.6 and 21.1 G-runs per thousand bp of vls coding strand, respectively, with no G-runs present on the non-coding strand. The conservation of this unprecedented distribution of G-runs on the vls coding strand between strains and between Lyme borriliae strongly argues for a functional role – especially when considering that G-rich codons are infrequently used in the A-T rich Borrelia genomes. The GGG glycine codon so prevalent within the G-runs is the least commonly used of the four (GGX) glycine codons in B. burgdorferi.


Suggested role for G4 DNA in recombinational switching at the antigenic variation locus of the Lyme disease spirochete.

Walia R, Chaconas G - PLoS ONE (2013)

Distribution of G3–5 runs on the linear plasmids carrying the vls loci in B. burgdorferi strains B31, N40 and JD1.G runs of 3–5 nucleotides in length were counted in the sequence of lp28-1 (Accession NC_001851 and FJ472338) from B31 [8], [52], [53], lp36 (Accession CP002230) from N40 and lp28-1 (Accession NC_017404) of JD1 [36]. The distribution of G3–5 runs on both strands of vls and non-vls DNA was plotted. The coding strand is defined as the strand in which the silent cassettes code for the VlsE protein. The vls DNA includes only the silent cassettes, as the vlsE sequence is only known for B31.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585125&req=5

pone-0057792-g007: Distribution of G3–5 runs on the linear plasmids carrying the vls loci in B. burgdorferi strains B31, N40 and JD1.G runs of 3–5 nucleotides in length were counted in the sequence of lp28-1 (Accession NC_001851 and FJ472338) from B31 [8], [52], [53], lp36 (Accession CP002230) from N40 and lp28-1 (Accession NC_017404) of JD1 [36]. The distribution of G3–5 runs on both strands of vls and non-vls DNA was plotted. The coding strand is defined as the strand in which the silent cassettes code for the VlsE protein. The vls DNA includes only the silent cassettes, as the vlsE sequence is only known for B31.
Mentions: G-runs are not present in the DR’s of other Lyme spirochetes and the DR’s are not believed to be involved in antigenic switching at vlsE (see Discussion). However, their ability to confer unusual properties upon the B31 vlsE locus in vitro, presumably through the formation of G4 DNA, prompted us to investigate the potential for formation of G4 DNA throughout the vls locus in several Lyme spirochetes. We analyzed the sequence of the linear plasmids carrying the vls locus from B. burgdorferi B31, N40 and JD1 [8], [36] for runs of G that were three or longer. These three strains show similar levels of divergence from one another with about 65% identity between vls cassettes [37] and contain clearly different DR’s within the silent cassettes [38]. Analysis of the B31 plasmid lp28-1, which carries the vls locus (Fig. 7), showed the presence of 2–3 G-runs per 1000 bp on either strand in the first 19,000 bp at the left end of the plasmid. In dramatic contrast, the vls region itself (8,239 bp) contained a total of 225 G-runs on the coding strand (27 runs per kb) and only one on the non-coding strand. This grossly unequal weighting of G-runs on the vls coding strand was also apparent on lp36 in strain N40 and on lp28-1 in strain JD1 (Fig. 7). Moreover, the somewhat more divergent vls regions from B. garinii Ip90 and B. afzelii ACA1 [38] also displayed 26.6 and 21.1 G-runs per thousand bp of vls coding strand, respectively, with no G-runs present on the non-coding strand. The conservation of this unprecedented distribution of G-runs on the vls coding strand between strains and between Lyme borriliae strongly argues for a functional role – especially when considering that G-rich codons are infrequently used in the A-T rich Borrelia genomes. The GGG glycine codon so prevalent within the G-runs is the least commonly used of the four (GGX) glycine codons in B. burgdorferi.

Bottom Line: In the work presented here we show that G4 DNA can be formed by sequences within the B31 vlsE locus, prompting us to investigate the presence of potential G4-forming DNA throughout the vls locus of several Lyme spirochete strains and species.We found that runs of G, three nucleotides and longer occur at a very high density, with a greater than 100-fold strand-specific distribution in the vls locus of three B. burgdorferi strains as well as in B. afzelii and B. garinii, in spite of the bias for the use of A-T rich codons in Borrelia species.Our findings suggest the possibility that G4 DNA may be a mediator of recombinational switching at the vlsE locus in the Lyme spirochetes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry & Molecular Biology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada.

ABSTRACT
Antigenic variation through targeted DNA rearrangements provides a powerful diversity generating mechanism that allows a variety of pathogens to stay one step ahead of acquired immunity in their hosts. The Lyme disease spirochete encodes such a system that is required for persistent infection. The vls locus, carried on a 29 kb linear plasmid (lp28-1) in the type strain B31, carries 15 silent cassettes from which information is unidirectionally transferred into the expression locus, vlsE. Recent studies have surprisingly shown that, with the exception of the RuvAB branch migrase, no other known recombination/repair proteins appear to play a role in the recombinational switching process. In the work presented here we show that G4 DNA can be formed by sequences within the B31 vlsE locus, prompting us to investigate the presence of potential G4-forming DNA throughout the vls locus of several Lyme spirochete strains and species. We found that runs of G, three nucleotides and longer occur at a very high density, with a greater than 100-fold strand-specific distribution in the vls locus of three B. burgdorferi strains as well as in B. afzelii and B. garinii, in spite of the bias for the use of A-T rich codons in Borrelia species. Our findings suggest the possibility that G4 DNA may be a mediator of recombinational switching at the vlsE locus in the Lyme spirochetes.

Show MeSH
Related in: MedlinePlus