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DNA topoisomerase VIII: a novel subfamily of type IIB topoisomerases encoded by free or integrated plasmids in Archaea and Bacteria.

Gadelle D, Krupovic M, Raymann K, Mayer C, Forterre P - Nucleic Acids Res. (2014)

Bottom Line: Purified topoisomerase VIII encoded by the plasmid pPPM1a from Paenibacillus polymyxa M1 had ATP-dependent relaxation and decatenation activities.In contrast, the enzyme encoded by mobile elements integrated into the genome of Ammonifex degensii exhibited DNA cleavage activity producing a full-length linear plasmid and that from Microscilla marina exhibited ATP-independent relaxation activity.Topoisomerases VIII, the smallest known type IIB enzymes, could be new promising models for structural and mechanistic studies.

View Article: PubMed Central - PubMed

Affiliation: Université Paris-Sud, CNRS UMR8621, Institut de Génétique Microbiologie, 91405 Orsay Cedex, France.

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Phylogeny of topoisomerase VIII. Bayesian phylogeny of the 24 topoisomerase VIII homologs listed in Supplementary Table S1 and two topoisomerase VIII enzymes detected in metagenomes (571 amino acid positions). The tree was calculated with MrBayes (MIX model + gamma4). The scale bar shows the average number of substitutions per site. Values at nodes are posterior probabilities and bootstrap values calculated with the rapid bootstrap feature of RAxML (LG + gamma4) from heuristic searches of 1000 resampled datasets, when the same node was recovered. Topoisomerase VIII enzymes encoded by a plasmid are marked by circles.
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Figure 3: Phylogeny of topoisomerase VIII. Bayesian phylogeny of the 24 topoisomerase VIII homologs listed in Supplementary Table S1 and two topoisomerase VIII enzymes detected in metagenomes (571 amino acid positions). The tree was calculated with MrBayes (MIX model + gamma4). The scale bar shows the average number of substitutions per site. Values at nodes are posterior probabilities and bootstrap values calculated with the rapid bootstrap feature of RAxML (LG + gamma4) from heuristic searches of 1000 resampled datasets, when the same node was recovered. Topoisomerase VIII enzymes encoded by a plasmid are marked by circles.

Mentions: Topoisomerase VIII is present in three bacterial phyla: Firmicutes (Clostridia and Bacilli), Bacteroidetes (Sphingobacteria) and Proteobacteria (alpha and gamma). Notably, those present in evolutionarily close genera are grouped together in phylogenetic analysis, whereas topoisomerase VIII enzymes from various genera of Proteobacteria and Firmicutes sometimes display mixed phylogenetic patterns (Figure 3). The three topoisomerase VIII enzymes encoded by plasmids are grouped with cellular topoisomerase VIII enzymes from species that are closely related to the hosts of these plasmids. For example, topoisomerase VIII enzymes encoded by pPPM1a and pPAV109 from P. polymyxa and P. alvei, respectively, are grouped with the chromosomally-encoded topoisomerase VIII from Paenibacillus panacisoli. Similarly, the topoisomerase VIII encoded by the plasmid from a haloarchaeon clusters with a sequence present in a metagenome from a hypersaline lake (Figure 3). These observations are consistent with previous studies that have shown that mobile elements often co-evolve with their hosts (35,36).


DNA topoisomerase VIII: a novel subfamily of type IIB topoisomerases encoded by free or integrated plasmids in Archaea and Bacteria.

Gadelle D, Krupovic M, Raymann K, Mayer C, Forterre P - Nucleic Acids Res. (2014)

Phylogeny of topoisomerase VIII. Bayesian phylogeny of the 24 topoisomerase VIII homologs listed in Supplementary Table S1 and two topoisomerase VIII enzymes detected in metagenomes (571 amino acid positions). The tree was calculated with MrBayes (MIX model + gamma4). The scale bar shows the average number of substitutions per site. Values at nodes are posterior probabilities and bootstrap values calculated with the rapid bootstrap feature of RAxML (LG + gamma4) from heuristic searches of 1000 resampled datasets, when the same node was recovered. Topoisomerase VIII enzymes encoded by a plasmid are marked by circles.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4117785&req=5

Figure 3: Phylogeny of topoisomerase VIII. Bayesian phylogeny of the 24 topoisomerase VIII homologs listed in Supplementary Table S1 and two topoisomerase VIII enzymes detected in metagenomes (571 amino acid positions). The tree was calculated with MrBayes (MIX model + gamma4). The scale bar shows the average number of substitutions per site. Values at nodes are posterior probabilities and bootstrap values calculated with the rapid bootstrap feature of RAxML (LG + gamma4) from heuristic searches of 1000 resampled datasets, when the same node was recovered. Topoisomerase VIII enzymes encoded by a plasmid are marked by circles.
Mentions: Topoisomerase VIII is present in three bacterial phyla: Firmicutes (Clostridia and Bacilli), Bacteroidetes (Sphingobacteria) and Proteobacteria (alpha and gamma). Notably, those present in evolutionarily close genera are grouped together in phylogenetic analysis, whereas topoisomerase VIII enzymes from various genera of Proteobacteria and Firmicutes sometimes display mixed phylogenetic patterns (Figure 3). The three topoisomerase VIII enzymes encoded by plasmids are grouped with cellular topoisomerase VIII enzymes from species that are closely related to the hosts of these plasmids. For example, topoisomerase VIII enzymes encoded by pPPM1a and pPAV109 from P. polymyxa and P. alvei, respectively, are grouped with the chromosomally-encoded topoisomerase VIII from Paenibacillus panacisoli. Similarly, the topoisomerase VIII encoded by the plasmid from a haloarchaeon clusters with a sequence present in a metagenome from a hypersaline lake (Figure 3). These observations are consistent with previous studies that have shown that mobile elements often co-evolve with their hosts (35,36).

Bottom Line: Purified topoisomerase VIII encoded by the plasmid pPPM1a from Paenibacillus polymyxa M1 had ATP-dependent relaxation and decatenation activities.In contrast, the enzyme encoded by mobile elements integrated into the genome of Ammonifex degensii exhibited DNA cleavage activity producing a full-length linear plasmid and that from Microscilla marina exhibited ATP-independent relaxation activity.Topoisomerases VIII, the smallest known type IIB enzymes, could be new promising models for structural and mechanistic studies.

View Article: PubMed Central - PubMed

Affiliation: Université Paris-Sud, CNRS UMR8621, Institut de Génétique Microbiologie, 91405 Orsay Cedex, France.

Show MeSH