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Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii.

Berglund EC, Frank AC, Calteau A, Vinnere Pettersson O, Granberg F, Eriksson AS, Näslund K, Holmberg M, Lindroos H, Andersson SG - PLoS Genet. (2009)

Bottom Line: Comparative genomics revealed that rodent-associated Bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens.Because of the high concentration of gene clusters for host-adaptation proteins in the amplified region, and since the genes encoding the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize that these systems are driven by selection.We propose that the coupling of run-off replication with gene transfer agents promotes diversification and rapid spread of host-adaptability factors, facilitating host shifts in Bartonella.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

ABSTRACT
The genus Bartonella comprises facultative intracellular bacteria adapted to mammals, including previously recognized and emerging human pathogens. We report the 2,341,328 bp genome sequence of Bartonella grahamii, one of the most prevalent Bartonella species in wild rodents. Comparative genomics revealed that rodent-associated Bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens. Many of these gene clusters are located in a highly dynamic region of 461 kb. Using hybridization to a microarray designed for the B. grahamii genome, we observed a massive, putatively phage-derived run-off replication of this region. We also identified a novel gene transfer agent, which packages the bacterial genome, with an over-representation of the amplified DNA, in 14 kb pieces. This is the first observation associating the products of run-off replication with a gene transfer agent. Because of the high concentration of gene clusters for host-adaptation proteins in the amplified region, and since the genes encoding the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize that these systems are driven by selection. We propose that the coupling of run-off replication with gene transfer agents promotes diversification and rapid spread of host-adaptability factors, facilitating host shifts in Bartonella.

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DNA content of B. grahamii bacteriophage particles.Results from microarray hybridizations of phage DNA versus cellular DNA of the same strain. The x-axis represents the genome of B. grahamii as4aup and the y-axis the hybridization signal (log2-ratio of phage DNA and cellular DNA). To exclude possible misinterpretation of repeated probes, probes with more than one exact match in the genome were not plotted unless located in the prophage regions. (A) Total phage DNA from B. grahamii as4aup. (B) Total phage DNA from B. grahamii af165up. Phage DNA extracted from (C) the 45 kb band and (D) the 14 kb band in agarose electrophoreses from B. grahamii af165up. Above the x-axis in all graphs is a representation of the genome of B. grahamii as4aup with the same color-coding as in Figure 1. In particular, phage genes are yellow. Grey dots in (C) and (D) show the result of the hybridization of total phage DNA from B. grahamii af165up (Figure 9B).
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pgen-1000546-g009: DNA content of B. grahamii bacteriophage particles.Results from microarray hybridizations of phage DNA versus cellular DNA of the same strain. The x-axis represents the genome of B. grahamii as4aup and the y-axis the hybridization signal (log2-ratio of phage DNA and cellular DNA). To exclude possible misinterpretation of repeated probes, probes with more than one exact match in the genome were not plotted unless located in the prophage regions. (A) Total phage DNA from B. grahamii as4aup. (B) Total phage DNA from B. grahamii af165up. Phage DNA extracted from (C) the 45 kb band and (D) the 14 kb band in agarose electrophoreses from B. grahamii af165up. Above the x-axis in all graphs is a representation of the genome of B. grahamii as4aup with the same color-coding as in Figure 1. In particular, phage genes are yellow. Grey dots in (C) and (D) show the result of the hybridization of total phage DNA from B. grahamii af165up (Figure 9B).

Mentions: To examine the gene content of the bacteriophage DNA, we constructed a microarray from 4,438 oligomers of 60 bp in size, which covers 1703 protein-coding genes (96% of the predicted protein-coding genes in B. grahamii), 110 pseudogenes and 663 intergenic regions. We hybridized bacteriophage DNA from B. grahamii strains as4aup and af165up against cellular DNA from the same strain harvested at the same time point. In both strains, we observed an increase in hybridization signal over the chromosomal high plasticity zone and until ori, with the strongest signal in the centre and gradually decreasing in both directions (Figure 9AB). The peak, at which the signal is approximately 30-fold stronger in the phage DNA compared to the cellular DNA, is located close to or within the helicase in phage cluster III (Figure 6D). This site is homologous to the site where the amplification peak was observed in hybridizations of genomic DNA from B. henselae [17]. In strain af165up, we observed a strong amplification of prophage I, which is also visible in strain as4aup but to a much smaller extent.


Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii.

Berglund EC, Frank AC, Calteau A, Vinnere Pettersson O, Granberg F, Eriksson AS, Näslund K, Holmberg M, Lindroos H, Andersson SG - PLoS Genet. (2009)

DNA content of B. grahamii bacteriophage particles.Results from microarray hybridizations of phage DNA versus cellular DNA of the same strain. The x-axis represents the genome of B. grahamii as4aup and the y-axis the hybridization signal (log2-ratio of phage DNA and cellular DNA). To exclude possible misinterpretation of repeated probes, probes with more than one exact match in the genome were not plotted unless located in the prophage regions. (A) Total phage DNA from B. grahamii as4aup. (B) Total phage DNA from B. grahamii af165up. Phage DNA extracted from (C) the 45 kb band and (D) the 14 kb band in agarose electrophoreses from B. grahamii af165up. Above the x-axis in all graphs is a representation of the genome of B. grahamii as4aup with the same color-coding as in Figure 1. In particular, phage genes are yellow. Grey dots in (C) and (D) show the result of the hybridization of total phage DNA from B. grahamii af165up (Figure 9B).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2697382&req=5

pgen-1000546-g009: DNA content of B. grahamii bacteriophage particles.Results from microarray hybridizations of phage DNA versus cellular DNA of the same strain. The x-axis represents the genome of B. grahamii as4aup and the y-axis the hybridization signal (log2-ratio of phage DNA and cellular DNA). To exclude possible misinterpretation of repeated probes, probes with more than one exact match in the genome were not plotted unless located in the prophage regions. (A) Total phage DNA from B. grahamii as4aup. (B) Total phage DNA from B. grahamii af165up. Phage DNA extracted from (C) the 45 kb band and (D) the 14 kb band in agarose electrophoreses from B. grahamii af165up. Above the x-axis in all graphs is a representation of the genome of B. grahamii as4aup with the same color-coding as in Figure 1. In particular, phage genes are yellow. Grey dots in (C) and (D) show the result of the hybridization of total phage DNA from B. grahamii af165up (Figure 9B).
Mentions: To examine the gene content of the bacteriophage DNA, we constructed a microarray from 4,438 oligomers of 60 bp in size, which covers 1703 protein-coding genes (96% of the predicted protein-coding genes in B. grahamii), 110 pseudogenes and 663 intergenic regions. We hybridized bacteriophage DNA from B. grahamii strains as4aup and af165up against cellular DNA from the same strain harvested at the same time point. In both strains, we observed an increase in hybridization signal over the chromosomal high plasticity zone and until ori, with the strongest signal in the centre and gradually decreasing in both directions (Figure 9AB). The peak, at which the signal is approximately 30-fold stronger in the phage DNA compared to the cellular DNA, is located close to or within the helicase in phage cluster III (Figure 6D). This site is homologous to the site where the amplification peak was observed in hybridizations of genomic DNA from B. henselae [17]. In strain af165up, we observed a strong amplification of prophage I, which is also visible in strain as4aup but to a much smaller extent.

Bottom Line: Comparative genomics revealed that rodent-associated Bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens.Because of the high concentration of gene clusters for host-adaptation proteins in the amplified region, and since the genes encoding the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize that these systems are driven by selection.We propose that the coupling of run-off replication with gene transfer agents promotes diversification and rapid spread of host-adaptability factors, facilitating host shifts in Bartonella.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

ABSTRACT
The genus Bartonella comprises facultative intracellular bacteria adapted to mammals, including previously recognized and emerging human pathogens. We report the 2,341,328 bp genome sequence of Bartonella grahamii, one of the most prevalent Bartonella species in wild rodents. Comparative genomics revealed that rodent-associated Bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens. Many of these gene clusters are located in a highly dynamic region of 461 kb. Using hybridization to a microarray designed for the B. grahamii genome, we observed a massive, putatively phage-derived run-off replication of this region. We also identified a novel gene transfer agent, which packages the bacterial genome, with an over-representation of the amplified DNA, in 14 kb pieces. This is the first observation associating the products of run-off replication with a gene transfer agent. Because of the high concentration of gene clusters for host-adaptation proteins in the amplified region, and since the genes encoding the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize that these systems are driven by selection. We propose that the coupling of run-off replication with gene transfer agents promotes diversification and rapid spread of host-adaptability factors, facilitating host shifts in Bartonella.

Show MeSH
Related in: MedlinePlus