Freshwater selenium-methylating bacterial thiopurine methyltransferases: diversity and molecular phylogeny.
The diversity of bacterial thiopurine methyltransferases (bTPMT) among five natural Se-methylating freshwaters was investigated by polymerase chain reaction (PCR) screenings and sequencings. DNA sequence analyses confirmed the cloned products' identity and revealed a broad diversity of freshwater TPMTs. Neighbour-joining (NJ) phylogenetic analyses combining these sequences, all GenBank entries closely related to these sequences and deduced TPMTs obtained in this work from selected gamma-proteobacteria showed TPMTs to form a distinct radiation, closely related to UbiG methyltransferases. Inside the TPMT phylogenetic cluster, eukaryote sequences diverged early from the bacterial ones, and all the bacterial database entries belonged to a subgroup of gamma-proteobacteria, with an apparent lateral transfer of a particular allele to beta-proteobacteria of Bordetella. The NJ phylogenetic tree revealed 22 bTPMT lineages, 10 of which harboured freshwater sequences. All lineages showed deep and long branches indicative of major genetic drifts outside regions encoding highly conserved domains. Selected residues among these highly variable domains could reflect adaptations for particular ecological niches. PCR lineage-specific primers differentiated Se-methylating freshwaters according to their 'tpm lineage' signatures. Most freshwater tpm alleles were found to be distinct from those available in the databases, but a group of tpm was found encoding TPMTs identical to an Aeromonas veronii TPMT characterized in this work.
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UMR CNRS UCBL 5557 Ecologie Microbienne (Center for Microbial Ecology), Research Group on Opportunistic Pathogens and Environment, Université Claude Bernard - Lyon 1, Mendel Bldg, 5th floor, 69622 Villeurbanne Cedex, France.
Ranjard
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Colinon
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Prigent-Combaret
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Nazaret
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Cournoyer
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D000333:Aeromonas; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics; D001483:Base Sequence; D001884:Bordetella; D016384:Consensus Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification; D029968:Escherichia coli Proteins / Q000235:genetics; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D008780:Methyltransferases / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary / Q000235:genetics; D012643:Selenium / Q000378:metabolism*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014871:Water Microbiology
D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D008780:Methyltransferases; C019616:UbiG protein, E coli; C022745:thiopurine methyltransferase; D012643:Selenium