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A high-resolution view of genome-wide pneumococcal transformation.

Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD - PLoS Pathog. (2012)

Bottom Line: Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes.However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA.The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1).

View Article: PubMed Central - PubMed

Affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. nc3@sanger.ac.uk

ABSTRACT
Transformation is an important mechanism of microbial evolution through which bacteria have been observed to rapidly adapt in response to clinical interventions; examples include facilitating vaccine evasion and the development of penicillin resistance in the major respiratory pathogen Streptococcus pneumoniae. To characterise the process in detail, the genomes of 124 S. pneumoniae isolates produced through in vitro transformation were sequenced and recombination events detected. Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes. However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA. The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1). This distribution of recombination sizes, coupled with an observed under representation of large insertions within transferred sequence, suggests transformation has the potential to reduce the size of bacterial genomes, and is unlikely to act as an efficient mechanism for the uptake of accessory genomic loci.

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Distribution of recombination sizes.(A) Histogram showing the distribution of RSS sizes as L50R lengths. The vertical green line shows the length of the cps locus in the recipient's genome (21,373 bp). The recombinations longer than this are the selected events importing the kanamycin resistance marker. The smaller, unselected recombinations are modelled as an exponential distribution (red line), with the calculated rate parameter displayed. (B) Histogram showing the distribution of donor molecule lengths participating in primary recombinations, as estimated using the L50D lengths of the NCR boundaries. The vertical green line shows the length of the kanamycin resistance locus in the donor DNA (1,354 bp). (C) Histogram showing the distribution of secondary RSS sizes as L50R lengths. These are modelled as an exponential distribution, indicated by the red line and displayed rate parameter. (D) Histogram showing the distribution of secondary NCR L50D lengths, thereby estimating the sizes of donor molecules participating in secondary recombinations. These are also modelled as an exponential distribution, indicated by the red line and annotated rate parameter.
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ppat-1002745-g004: Distribution of recombination sizes.(A) Histogram showing the distribution of RSS sizes as L50R lengths. The vertical green line shows the length of the cps locus in the recipient's genome (21,373 bp). The recombinations longer than this are the selected events importing the kanamycin resistance marker. The smaller, unselected recombinations are modelled as an exponential distribution (red line), with the calculated rate parameter displayed. (B) Histogram showing the distribution of donor molecule lengths participating in primary recombinations, as estimated using the L50D lengths of the NCR boundaries. The vertical green line shows the length of the kanamycin resistance locus in the donor DNA (1,354 bp). (C) Histogram showing the distribution of secondary RSS sizes as L50R lengths. These are modelled as an exponential distribution, indicated by the red line and displayed rate parameter. (D) Histogram showing the distribution of secondary NCR L50D lengths, thereby estimating the sizes of donor molecules participating in secondary recombinations. These are also modelled as an exponential distribution, indicated by the red line and annotated rate parameter.

Mentions: A histogram of the L50R values for recombinations within the primary locus reveals the selected and unselected RSSs have very different size distributions (Figure 4A). The unselected RSSs are typically less than 5 kb in length, and follow an approximately exponential distribution with a rate constant, λR, of 4.96×10−4 bp−1 (95% confidence interval 3.60–7.23×10−4 bp−1). Those spanning the cps locus are longer (and therefore estimate λR as being smaller), due to the necessity of spanning the 21,373 bp gene cluster, and follow a different size distribution, as the probability of transmitting the selectable marker to the recipient rises as the length of the recombination increases [47]. The size distribution of the imported strand, which can be calculated on the basis that all primary RSSs originate from the same DNA molecule, is similar (Figure 4B). The median L50D of these values was found to be 5.9 kb, comparable to the median imported strand length of ∼6.6 kb [9] despite the size constraint of importing the kanamycin resistance gene.


A high-resolution view of genome-wide pneumococcal transformation.

Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD - PLoS Pathog. (2012)

Distribution of recombination sizes.(A) Histogram showing the distribution of RSS sizes as L50R lengths. The vertical green line shows the length of the cps locus in the recipient's genome (21,373 bp). The recombinations longer than this are the selected events importing the kanamycin resistance marker. The smaller, unselected recombinations are modelled as an exponential distribution (red line), with the calculated rate parameter displayed. (B) Histogram showing the distribution of donor molecule lengths participating in primary recombinations, as estimated using the L50D lengths of the NCR boundaries. The vertical green line shows the length of the kanamycin resistance locus in the donor DNA (1,354 bp). (C) Histogram showing the distribution of secondary RSS sizes as L50R lengths. These are modelled as an exponential distribution, indicated by the red line and displayed rate parameter. (D) Histogram showing the distribution of secondary NCR L50D lengths, thereby estimating the sizes of donor molecules participating in secondary recombinations. These are also modelled as an exponential distribution, indicated by the red line and annotated rate parameter.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3375284&req=5

ppat-1002745-g004: Distribution of recombination sizes.(A) Histogram showing the distribution of RSS sizes as L50R lengths. The vertical green line shows the length of the cps locus in the recipient's genome (21,373 bp). The recombinations longer than this are the selected events importing the kanamycin resistance marker. The smaller, unselected recombinations are modelled as an exponential distribution (red line), with the calculated rate parameter displayed. (B) Histogram showing the distribution of donor molecule lengths participating in primary recombinations, as estimated using the L50D lengths of the NCR boundaries. The vertical green line shows the length of the kanamycin resistance locus in the donor DNA (1,354 bp). (C) Histogram showing the distribution of secondary RSS sizes as L50R lengths. These are modelled as an exponential distribution, indicated by the red line and displayed rate parameter. (D) Histogram showing the distribution of secondary NCR L50D lengths, thereby estimating the sizes of donor molecules participating in secondary recombinations. These are also modelled as an exponential distribution, indicated by the red line and annotated rate parameter.
Mentions: A histogram of the L50R values for recombinations within the primary locus reveals the selected and unselected RSSs have very different size distributions (Figure 4A). The unselected RSSs are typically less than 5 kb in length, and follow an approximately exponential distribution with a rate constant, λR, of 4.96×10−4 bp−1 (95% confidence interval 3.60–7.23×10−4 bp−1). Those spanning the cps locus are longer (and therefore estimate λR as being smaller), due to the necessity of spanning the 21,373 bp gene cluster, and follow a different size distribution, as the probability of transmitting the selectable marker to the recipient rises as the length of the recombination increases [47]. The size distribution of the imported strand, which can be calculated on the basis that all primary RSSs originate from the same DNA molecule, is similar (Figure 4B). The median L50D of these values was found to be 5.9 kb, comparable to the median imported strand length of ∼6.6 kb [9] despite the size constraint of importing the kanamycin resistance gene.

Bottom Line: Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes.However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA.The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1).

View Article: PubMed Central - PubMed

Affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. nc3@sanger.ac.uk

ABSTRACT
Transformation is an important mechanism of microbial evolution through which bacteria have been observed to rapidly adapt in response to clinical interventions; examples include facilitating vaccine evasion and the development of penicillin resistance in the major respiratory pathogen Streptococcus pneumoniae. To characterise the process in detail, the genomes of 124 S. pneumoniae isolates produced through in vitro transformation were sequenced and recombination events detected. Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes. However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA. The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1). This distribution of recombination sizes, coupled with an observed under representation of large insertions within transferred sequence, suggests transformation has the potential to reduce the size of bacterial genomes, and is unlikely to act as an efficient mechanism for the uptake of accessory genomic loci.

Show MeSH
Related in: MedlinePlus