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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 events across the genome.(A) Cartoon describing the structure of RSSs as discussed in the text. (B) A detailed view of the RSSs spanning and surrounding the cps locus. The annotation of the region is shown at the top, with the cps locus and flanking pbp genes marked. The red line denotes the extent of the ‘primary locus’ (see text). Underneath, in the panel indicated by the dashed boundary, the RSSs affecting this locus are indicated on the rows by black and grey blocks, as displayed in panel (A). There is a row for each of the 84 transformants, segregated according to the amount of DNA with which they were transformed. (C) Wider view of recombination across the genome. A simplified annotation of the 2,182,009 bp S. pneumoniae 23F-R genome is displayed across the top, with the site of the selected recombination (the cps locus) labelled along with other major chromosomal loci. The RSSs are displayed as indicated in panel (A), with the strains in the same order as in panel (B).
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ppat-1002745-g002: Distribution of recombination events across the genome.(A) Cartoon describing the structure of RSSs as discussed in the text. (B) A detailed view of the RSSs spanning and surrounding the cps locus. The annotation of the region is shown at the top, with the cps locus and flanking pbp genes marked. The red line denotes the extent of the ‘primary locus’ (see text). Underneath, in the panel indicated by the dashed boundary, the RSSs affecting this locus are indicated on the rows by black and grey blocks, as displayed in panel (A). There is a row for each of the 84 transformants, segregated according to the amount of DNA with which they were transformed. (C) Wider view of recombination across the genome. A simplified annotation of the 2,182,009 bp S. pneumoniae 23F-R genome is displayed across the top, with the site of the selected recombination (the cps locus) labelled along with other major chromosomal loci. The RSSs are displayed as indicated in panel (A), with the strains in the same order as in panel (B).

Mentions: Recombinant sequence segments (RSSs) were detectable as loci containing donor alleles at polymorphic sites, defining the minimum size of the recombination, bounded by recipient alleles at the flanking polymorphic sites, demarcating the maximum size of the exchange (Figure 2A). The actual length may be estimated as being the median (L50) between these two limits, positioning the flanks half way through each boundary region (BR). As with the separation between any two loci, this length can be expressed either as a distance relative to the donor (L50D) or recipient (L50R) genome, which differ where there are sequence insertions distinguishing the strains. The selected recombination at the cps locus was detected in all transformants. In order to distinguish those events driven by selection from those elsewhere in the chromosome, a ‘primary locus’, encompassing the cps region, was defined between the genomic loci 294,383 bp and 340,516 bp in strain 23F-R: all bases between these coordinates had undergone recombination in at least one of the 84 sequenced isolates (Figure 2B).


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 events across the genome.(A) Cartoon describing the structure of RSSs as discussed in the text. (B) A detailed view of the RSSs spanning and surrounding the cps locus. The annotation of the region is shown at the top, with the cps locus and flanking pbp genes marked. The red line denotes the extent of the ‘primary locus’ (see text). Underneath, in the panel indicated by the dashed boundary, the RSSs affecting this locus are indicated on the rows by black and grey blocks, as displayed in panel (A). There is a row for each of the 84 transformants, segregated according to the amount of DNA with which they were transformed. (C) Wider view of recombination across the genome. A simplified annotation of the 2,182,009 bp S. pneumoniae 23F-R genome is displayed across the top, with the site of the selected recombination (the cps locus) labelled along with other major chromosomal loci. The RSSs are displayed as indicated in panel (A), with the strains in the same order as in panel (B).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3375284&req=5

ppat-1002745-g002: Distribution of recombination events across the genome.(A) Cartoon describing the structure of RSSs as discussed in the text. (B) A detailed view of the RSSs spanning and surrounding the cps locus. The annotation of the region is shown at the top, with the cps locus and flanking pbp genes marked. The red line denotes the extent of the ‘primary locus’ (see text). Underneath, in the panel indicated by the dashed boundary, the RSSs affecting this locus are indicated on the rows by black and grey blocks, as displayed in panel (A). There is a row for each of the 84 transformants, segregated according to the amount of DNA with which they were transformed. (C) Wider view of recombination across the genome. A simplified annotation of the 2,182,009 bp S. pneumoniae 23F-R genome is displayed across the top, with the site of the selected recombination (the cps locus) labelled along with other major chromosomal loci. The RSSs are displayed as indicated in panel (A), with the strains in the same order as in panel (B).
Mentions: Recombinant sequence segments (RSSs) were detectable as loci containing donor alleles at polymorphic sites, defining the minimum size of the recombination, bounded by recipient alleles at the flanking polymorphic sites, demarcating the maximum size of the exchange (Figure 2A). The actual length may be estimated as being the median (L50) between these two limits, positioning the flanks half way through each boundary region (BR). As with the separation between any two loci, this length can be expressed either as a distance relative to the donor (L50D) or recipient (L50R) genome, which differ where there are sequence insertions distinguishing the strains. The selected recombination at the cps locus was detected in all transformants. In order to distinguish those events driven by selection from those elsewhere in the chromosome, a ‘primary locus’, encompassing the cps region, was defined between the genomic loci 294,383 bp and 340,516 bp in strain 23F-R: all bases between these coordinates had undergone recombination in at least one of the 84 sequenced isolates (Figure 2B).

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