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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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CAGs families. In this figure, each circle correspond to either a plasmid (pT26-2) or to an integrated element identified as a cluster of atypical genes (41). Each link between two elements means that they share at least five homologous genes (see ‘Materials and Methods’ section for further details). The plasmid pT26-2 is in black, and the other Thermococcales integrated elements are in dark grey (TKV1, TKV2, TKV3, PHV1). The integrated elements sharing core genes with pT26-2 (described in the text), are linked by bold lines. Integrated elements from Methanococcales are represented in light grey whereas integrated elements from other phyla (Methanosarcinales and Nanoarchaea) are represented in grey.
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Figure 4: CAGs families. In this figure, each circle correspond to either a plasmid (pT26-2) or to an integrated element identified as a cluster of atypical genes (41). Each link between two elements means that they share at least five homologous genes (see ‘Materials and Methods’ section for further details). The plasmid pT26-2 is in black, and the other Thermococcales integrated elements are in dark grey (TKV1, TKV2, TKV3, PHV1). The integrated elements sharing core genes with pT26-2 (described in the text), are linked by bold lines. Integrated elements from Methanococcales are represented in light grey whereas integrated elements from other phyla (Methanosarcinales and Nanoarchaea) are represented in grey.

Mentions: To get clue about possible more distant evolutionary relationships between members of the pT26-2 family and other plasmids and virus-like elements integrated in archaeal genomes (previously identified as CAGs, 41), we have draw different networks in which two elements are linked to each other by a line if they share either three, four or five genes (threshold) and a bold line if they share the seven core genes of the pT26-2 family. Interestingly, members of the pT26-2 family become linked to more and more CAGs or to free plasmids when the threshold was reduced from five to two (Figure 4 and S11B-E). Whereas pT26-2 was only linked to CAGs or plasmids from Thermococcales and Methanococcales with a threshold of five, it became also linked to Methanosarcinales with a threshold of four. Finally, when the threshold was relaxed to three, CAGs from Thermoplasmatales and Halobacteriales were recruited into the network of plasmid/CAG interactions and several large families are clearly delineated (plasmids from halobacterial were removed from this analysis because their high number introduced a bias). This analysis thus defines a huge superfamily of mobile elements loosely related to pT26-2 that encompass the whole phylum of Euryarchaea. Sulfolobales (phylum Crenarchaea) only entered into the network when the threshold was reduced to two.Figure 4.


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)

CAGs families. In this figure, each circle correspond to either a plasmid (pT26-2) or to an integrated element identified as a cluster of atypical genes (41). Each link between two elements means that they share at least five homologous genes (see ‘Materials and Methods’ section for further details). The plasmid pT26-2 is in black, and the other Thermococcales integrated elements are in dark grey (TKV1, TKV2, TKV3, PHV1). The integrated elements sharing core genes with pT26-2 (described in the text), are linked by bold lines. Integrated elements from Methanococcales are represented in light grey whereas integrated elements from other phyla (Methanosarcinales and Nanoarchaea) are represented in grey.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: CAGs families. In this figure, each circle correspond to either a plasmid (pT26-2) or to an integrated element identified as a cluster of atypical genes (41). Each link between two elements means that they share at least five homologous genes (see ‘Materials and Methods’ section for further details). The plasmid pT26-2 is in black, and the other Thermococcales integrated elements are in dark grey (TKV1, TKV2, TKV3, PHV1). The integrated elements sharing core genes with pT26-2 (described in the text), are linked by bold lines. Integrated elements from Methanococcales are represented in light grey whereas integrated elements from other phyla (Methanosarcinales and Nanoarchaea) are represented in grey.
Mentions: To get clue about possible more distant evolutionary relationships between members of the pT26-2 family and other plasmids and virus-like elements integrated in archaeal genomes (previously identified as CAGs, 41), we have draw different networks in which two elements are linked to each other by a line if they share either three, four or five genes (threshold) and a bold line if they share the seven core genes of the pT26-2 family. Interestingly, members of the pT26-2 family become linked to more and more CAGs or to free plasmids when the threshold was reduced from five to two (Figure 4 and S11B-E). Whereas pT26-2 was only linked to CAGs or plasmids from Thermococcales and Methanococcales with a threshold of five, it became also linked to Methanosarcinales with a threshold of four. Finally, when the threshold was relaxed to three, CAGs from Thermoplasmatales and Halobacteriales were recruited into the network of plasmid/CAG interactions and several large families are clearly delineated (plasmids from halobacterial were removed from this analysis because their high number introduced a bias). This analysis thus defines a huge superfamily of mobile elements loosely related to pT26-2 that encompass the whole phylum of Euryarchaea. Sulfolobales (phylum Crenarchaea) only entered into the network when the threshold was reduced to two.Figure 4.

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