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Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins.

Soler N, Marguet E, Cortez D, Desnoues N, Keller J, van Tilbeurgh H, Sezonov G, Forterre P - Nucleic Acids Res. (2010)

Bottom Line: The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales.Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism.The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase.

View Article: PubMed Central - PubMed

Affiliation: Institut de Génétique et Microbiologie, Univ Paris-Sud, Orsay, France. nicolas.soler@inserm.fr

ABSTRACT
Thermococcales (phylum Euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. Here we describe three new plasmids from Thermococcales that could provide new tools and model systems for genetic and molecular studies in Archaea. The plasmids pTN2 from Thermococcus nautilus sp. 30-1 and pP12-1 from Pyrococcus sp. 12-1 belong to the same family. They have similar size (approximately 12 kb) and share six genes, including homologues of genes encoded by the virus PAV1 from Pyrococcus abyssi. The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales. Our analyses confirm that viruses and plasmids are evolutionary related and co-evolve with their hosts. Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism. The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase. This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication.

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Schematic representation of the three new plasmids. (A) pTN2 and pP12-1 plasmid maps were drawn at the same scale together with PAV1 genome. ORFs are numbered and represented as arrows. ORFs encoding homologous proteins have the same colour. White ORFs do not have detectable homologues among these three genomes. (B) pT26-2 plasmid map with ORFs numbered and represented as arrows. Coloured ORFs encode proteins with expected activity or function. (A and B) Hachured ORFs harbour putative hydrophobic segments. Circles indicate large intergenic regions including putative replication origins.
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Figure 1: Schematic representation of the three new plasmids. (A) pTN2 and pP12-1 plasmid maps were drawn at the same scale together with PAV1 genome. ORFs are numbered and represented as arrows. ORFs encoding homologous proteins have the same colour. White ORFs do not have detectable homologues among these three genomes. (B) pT26-2 plasmid map with ORFs numbered and represented as arrows. Coloured ORFs encode proteins with expected activity or function. (A and B) Hachured ORFs harbour putative hydrophobic segments. Circles indicate large intergenic regions including putative replication origins.

Mentions: All ORFs of pTN2 and pP12-1 are located on the same DNA strand with only two exceptions detected in pP12-1. Similarly, 30 of the 32 pT26-2 ORFs are transcribed in the same direction (Figure 1). We predicted the position of the replication origin of these three plasmids by performing cumulative GC skew analysis (34). This method is based on the general observation that GC content usually differ between the leading and lagging strands of replication forks (35). The cumulative GC skews graphics for the three plasmids show GC frequency inversion producing V-like curves. Strikingly, the minima (blue arrows, Supplementary Figure S1) are located in the larger intergenic regions for each of the three plasmids (circles, Figure 1). These intergenic regions are among the most AT-rich of the three plasmids and contain many direct and inverted repeats; features that are general characteristics of plasmid replication origins (Supplementary Figure S2). Interestingly, the predicted origin regions of pP12-1 and pT26-2 are located close to ORFs (p12-14p, p12-12p and t26-19p) that are transcribed in the direction opposite to most other ORFs encoded by these plasmids (Figure 1).Figure 1.


Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins.

Soler N, Marguet E, Cortez D, Desnoues N, Keller J, van Tilbeurgh H, Sezonov G, Forterre P - Nucleic Acids Res. (2010)

Schematic representation of the three new plasmids. (A) pTN2 and pP12-1 plasmid maps were drawn at the same scale together with PAV1 genome. ORFs are numbered and represented as arrows. ORFs encoding homologous proteins have the same colour. White ORFs do not have detectable homologues among these three genomes. (B) pT26-2 plasmid map with ORFs numbered and represented as arrows. Coloured ORFs encode proteins with expected activity or function. (A and B) Hachured ORFs harbour putative hydrophobic segments. Circles indicate large intergenic regions including putative replication origins.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2926602&req=5

Figure 1: Schematic representation of the three new plasmids. (A) pTN2 and pP12-1 plasmid maps were drawn at the same scale together with PAV1 genome. ORFs are numbered and represented as arrows. ORFs encoding homologous proteins have the same colour. White ORFs do not have detectable homologues among these three genomes. (B) pT26-2 plasmid map with ORFs numbered and represented as arrows. Coloured ORFs encode proteins with expected activity or function. (A and B) Hachured ORFs harbour putative hydrophobic segments. Circles indicate large intergenic regions including putative replication origins.
Mentions: All ORFs of pTN2 and pP12-1 are located on the same DNA strand with only two exceptions detected in pP12-1. Similarly, 30 of the 32 pT26-2 ORFs are transcribed in the same direction (Figure 1). We predicted the position of the replication origin of these three plasmids by performing cumulative GC skew analysis (34). This method is based on the general observation that GC content usually differ between the leading and lagging strands of replication forks (35). The cumulative GC skews graphics for the three plasmids show GC frequency inversion producing V-like curves. Strikingly, the minima (blue arrows, Supplementary Figure S1) are located in the larger intergenic regions for each of the three plasmids (circles, Figure 1). These intergenic regions are among the most AT-rich of the three plasmids and contain many direct and inverted repeats; features that are general characteristics of plasmid replication origins (Supplementary Figure S2). Interestingly, the predicted origin regions of pP12-1 and pT26-2 are located close to ORFs (p12-14p, p12-12p and t26-19p) that are transcribed in the direction opposite to most other ORFs encoded by these plasmids (Figure 1).Figure 1.

Bottom Line: The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales.Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism.The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase.

View Article: PubMed Central - PubMed

Affiliation: Institut de Génétique et Microbiologie, Univ Paris-Sud, Orsay, France. nicolas.soler@inserm.fr

ABSTRACT
Thermococcales (phylum Euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. Here we describe three new plasmids from Thermococcales that could provide new tools and model systems for genetic and molecular studies in Archaea. The plasmids pTN2 from Thermococcus nautilus sp. 30-1 and pP12-1 from Pyrococcus sp. 12-1 belong to the same family. They have similar size (approximately 12 kb) and share six genes, including homologues of genes encoded by the virus PAV1 from Pyrococcus abyssi. The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales. Our analyses confirm that viruses and plasmids are evolutionary related and co-evolve with their hosts. Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism. The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase. This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication.

Show MeSH
Related in: MedlinePlus