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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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Related in: MedlinePlus

Growth curve of B. grahamii af165up.Growth curve of B. grahamii strain af165up in supplemented Schneider's medium. Bacterial growth was determined by measuring the OD600 in triplicates (grey line) and by quantifying the number of viable bacteria, expressed as CFU/ml (black line), at 24-h intervals. Samples were collected at the mid-logarithmic growth phase (day 2), the stationary phase (day 5), and at the end of the death phase (day 11).
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pgen-1000546-g010: Growth curve of B. grahamii af165up.Growth curve of B. grahamii strain af165up in supplemented Schneider's medium. Bacterial growth was determined by measuring the OD600 in triplicates (grey line) and by quantifying the number of viable bacteria, expressed as CFU/ml (black line), at 24-h intervals. Samples were collected at the mid-logarithmic growth phase (day 2), the stationary phase (day 5), and at the end of the death phase (day 11).

Mentions: To examine whether induction of the prophage and run-off replication occur predominantly in dying cells, or possibly is the cause of bacterial death, we collected phage particles from three different time points from a liquid culture of B. grahamii strain af165up, selected to represent exponential growth phase (growing, viable), stationary phase (non-growing, viable) and death phase (non-growing, non-viable) (Figure 10). We extracted phage DNA from each time point to hybridize against chromosomal DNA extracted from the exponential growth phase. To obtain enough DNA for the hybridization experiments, we amplified the phage DNA using whole genome amplification. This procedure will reveal differences in the relative abundance of different genes in the phage versus the chromosomal DNA samples, but does not show differences in the total amount of phage DNA produced at the three growth stages. The results showed clearly that replication of prophage I is initiated already during the exponential growth phase with prophage DNA being over-represented in the phage particles at all three time points (Figure 11). Likewise, the products of run-off replication were present in relatively higher quantities in the isolated phage particles than in the preparations of chromosomal DNA at all time points.


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)

Growth curve of B. grahamii af165up.Growth curve of B. grahamii strain af165up in supplemented Schneider's medium. Bacterial growth was determined by measuring the OD600 in triplicates (grey line) and by quantifying the number of viable bacteria, expressed as CFU/ml (black line), at 24-h intervals. Samples were collected at the mid-logarithmic growth phase (day 2), the stationary phase (day 5), and at the end of the death phase (day 11).
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000546-g010: Growth curve of B. grahamii af165up.Growth curve of B. grahamii strain af165up in supplemented Schneider's medium. Bacterial growth was determined by measuring the OD600 in triplicates (grey line) and by quantifying the number of viable bacteria, expressed as CFU/ml (black line), at 24-h intervals. Samples were collected at the mid-logarithmic growth phase (day 2), the stationary phase (day 5), and at the end of the death phase (day 11).
Mentions: To examine whether induction of the prophage and run-off replication occur predominantly in dying cells, or possibly is the cause of bacterial death, we collected phage particles from three different time points from a liquid culture of B. grahamii strain af165up, selected to represent exponential growth phase (growing, viable), stationary phase (non-growing, viable) and death phase (non-growing, non-viable) (Figure 10). We extracted phage DNA from each time point to hybridize against chromosomal DNA extracted from the exponential growth phase. To obtain enough DNA for the hybridization experiments, we amplified the phage DNA using whole genome amplification. This procedure will reveal differences in the relative abundance of different genes in the phage versus the chromosomal DNA samples, but does not show differences in the total amount of phage DNA produced at the three growth stages. The results showed clearly that replication of prophage I is initiated already during the exponential growth phase with prophage DNA being over-represented in the phage particles at all three time points (Figure 11). Likewise, the products of run-off replication were present in relatively higher quantities in the isolated phage particles than in the preparations of chromosomal DNA at all time points.

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