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The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism.

Martinsohn JT, Radman M, Petit MA - PLoS Genet. (2008)

Bottom Line: However, the precise molecular processes underlying this mosaicism are unknown.To test this, we have measured the efficiency of homeologous recombination between diverged oxa gene pairs inserted into lambda.The recombination editing proteins, MutS and UvrD, showed only marginal effects on lambda recombination.

View Article: PubMed Central - PubMed

Affiliation: Faculté de Médecine R. Descartes, INSERM U571, Université Paris Descartes, Paris, France.

ABSTRACT
Genome mosaicism in temperate bacterial viruses (bacteriophages) is so great that it obscures their phylogeny at the genome level. However, the precise molecular processes underlying this mosaicism are unknown. Illegitimate recombination has been proposed, but homeologous recombination could also be at play. To test this, we have measured the efficiency of homeologous recombination between diverged oxa gene pairs inserted into lambda. High yields of recombinants between 22% diverged genes have been obtained when the virus Red Gam pathway was active, and 100 fold less when the host Escherichia coli RecABCD pathway was active. The recombination editing proteins, MutS and UvrD, showed only marginal effects on lambda recombination. Thus, escape from host editing contributes to the high proficiency of virus recombination. Moreover, our bioinformatics study suggests that homeologous recombination between similar lambdoid viruses has created part of their mosaicism. We therefore propose that the remarkable propensity of the lambda-encoded Red and Gam proteins to recombine diverged DNA is effectively contributing to mosaicism, and more generally, that a correlation may exist between virus genome mosaicism and the presence of Red/Gam-like systems.

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Generation of an inversion between the oxa sequences.Left panel: two successive, non reciprocal events: Oxa sequences are shown with oriented boxes, dark and light gray. Step 1, a broken piece containing the rightward copy of oxa recombines with intact DNA, and generates an unviable molecule (step2), which in turn recombines its leftward oxa copy with another oxa sequence (step 3). This other broken piece eventually, but not necessarily, consists of the rest of the broken piece shown in step 1. Recombination gives rise to a viable product where the intermediate sequences have been inverted, and the two oxa genes are hybrids (step 4). A and R designate the leftmost and righmost genes of λ. Right panel: one reciprocal event. A crossing over is initiated intra-molecularly between the oxa sequences (step 1), and gives rise to the inverted configuration (step 2).
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pgen-1000065-g003: Generation of an inversion between the oxa sequences.Left panel: two successive, non reciprocal events: Oxa sequences are shown with oriented boxes, dark and light gray. Step 1, a broken piece containing the rightward copy of oxa recombines with intact DNA, and generates an unviable molecule (step2), which in turn recombines its leftward oxa copy with another oxa sequence (step 3). This other broken piece eventually, but not necessarily, consists of the rest of the broken piece shown in step 1. Recombination gives rise to a viable product where the intermediate sequences have been inverted, and the two oxa genes are hybrids (step 4). A and R designate the leftmost and righmost genes of λ. Right panel: one reciprocal event. A crossing over is initiated intra-molecularly between the oxa sequences (step 1), and gives rise to the inverted configuration (step 2).

Mentions: The presence of 32 and 176 sites of polymorphism for the oxa7-oxa11 and oxa7-oxa5 pairs, respectively, allowed us to map precisely strand exchanges and to class recombination events into two main categories: the “non-symmetrical” ones, for which the two joints are present in different intervals, and the “symmetrical” ones, for which the two joints occur in the same interval. Category “complex” includes more complex sequence patterns. Bacteriophage λ recombines essentially in a non-reciprocal mode, but in our recombination assay, only the events that terminate as reciprocal at the DNA level can yield viable recombinants. However, such ‘final’ reciprocity can be reached by two successive non-reciprocal events [39],[40], as shown on Figure 3, left panel. The two events being independent, most products are expected to be of the non-symmetrical category. If, under some conditions, λ recombines in a reciprocal mode at the molecular level, by a simple crossing-over, as shown in Figure 3, right panel, approximately half of the products, those derived from the RuvC-cut strand, are expected to be of the symmetrical category (see Discussion).


The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism.

Martinsohn JT, Radman M, Petit MA - PLoS Genet. (2008)

Generation of an inversion between the oxa sequences.Left panel: two successive, non reciprocal events: Oxa sequences are shown with oriented boxes, dark and light gray. Step 1, a broken piece containing the rightward copy of oxa recombines with intact DNA, and generates an unviable molecule (step2), which in turn recombines its leftward oxa copy with another oxa sequence (step 3). This other broken piece eventually, but not necessarily, consists of the rest of the broken piece shown in step 1. Recombination gives rise to a viable product where the intermediate sequences have been inverted, and the two oxa genes are hybrids (step 4). A and R designate the leftmost and righmost genes of λ. Right panel: one reciprocal event. A crossing over is initiated intra-molecularly between the oxa sequences (step 1), and gives rise to the inverted configuration (step 2).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2327257&req=5

pgen-1000065-g003: Generation of an inversion between the oxa sequences.Left panel: two successive, non reciprocal events: Oxa sequences are shown with oriented boxes, dark and light gray. Step 1, a broken piece containing the rightward copy of oxa recombines with intact DNA, and generates an unviable molecule (step2), which in turn recombines its leftward oxa copy with another oxa sequence (step 3). This other broken piece eventually, but not necessarily, consists of the rest of the broken piece shown in step 1. Recombination gives rise to a viable product where the intermediate sequences have been inverted, and the two oxa genes are hybrids (step 4). A and R designate the leftmost and righmost genes of λ. Right panel: one reciprocal event. A crossing over is initiated intra-molecularly between the oxa sequences (step 1), and gives rise to the inverted configuration (step 2).
Mentions: The presence of 32 and 176 sites of polymorphism for the oxa7-oxa11 and oxa7-oxa5 pairs, respectively, allowed us to map precisely strand exchanges and to class recombination events into two main categories: the “non-symmetrical” ones, for which the two joints are present in different intervals, and the “symmetrical” ones, for which the two joints occur in the same interval. Category “complex” includes more complex sequence patterns. Bacteriophage λ recombines essentially in a non-reciprocal mode, but in our recombination assay, only the events that terminate as reciprocal at the DNA level can yield viable recombinants. However, such ‘final’ reciprocity can be reached by two successive non-reciprocal events [39],[40], as shown on Figure 3, left panel. The two events being independent, most products are expected to be of the non-symmetrical category. If, under some conditions, λ recombines in a reciprocal mode at the molecular level, by a simple crossing-over, as shown in Figure 3, right panel, approximately half of the products, those derived from the RuvC-cut strand, are expected to be of the symmetrical category (see Discussion).

Bottom Line: However, the precise molecular processes underlying this mosaicism are unknown.To test this, we have measured the efficiency of homeologous recombination between diverged oxa gene pairs inserted into lambda.The recombination editing proteins, MutS and UvrD, showed only marginal effects on lambda recombination.

View Article: PubMed Central - PubMed

Affiliation: Faculté de Médecine R. Descartes, INSERM U571, Université Paris Descartes, Paris, France.

ABSTRACT
Genome mosaicism in temperate bacterial viruses (bacteriophages) is so great that it obscures their phylogeny at the genome level. However, the precise molecular processes underlying this mosaicism are unknown. Illegitimate recombination has been proposed, but homeologous recombination could also be at play. To test this, we have measured the efficiency of homeologous recombination between diverged oxa gene pairs inserted into lambda. High yields of recombinants between 22% diverged genes have been obtained when the virus Red Gam pathway was active, and 100 fold less when the host Escherichia coli RecABCD pathway was active. The recombination editing proteins, MutS and UvrD, showed only marginal effects on lambda recombination. Thus, escape from host editing contributes to the high proficiency of virus recombination. Moreover, our bioinformatics study suggests that homeologous recombination between similar lambdoid viruses has created part of their mosaicism. We therefore propose that the remarkable propensity of the lambda-encoded Red and Gam proteins to recombine diverged DNA is effectively contributing to mosaicism, and more generally, that a correlation may exist between virus genome mosaicism and the presence of Red/Gam-like systems.

Show MeSH
Related in: MedlinePlus