Deinococcus
Division >>> Thermus/Deinococcus group
>> Order Deinococcales > Genus Deinococcus
>> Order Thermales > Genus Thermus
Deinococcales Deinococcus
Thermales Thermus Meiothermus Marinithermus Oceanithermus Vulcanithermus
(tem Deinococcus radiodurans) Conan the Bacterium Metabolic pathways D. radiodurans
D. radiodurans
Phylogenetic diversity of the deinococci as determined by 16S ribosomal DNA sequence comparison
Genome trees constructed using five different approaches suggest new major bacterial clades.
Five largely independent approaches were employed to construct trees for completely sequenced bacterial and archaeal genomes: i) presence-absence of genomes in clusters of orthologous genes; ii) conservation of local gene order (gene pairs) among prokaryotic genomes; iii) parameters of identity distribution for probable orthologs; iv) analysis of concatenated alignments of ribosomal proteins; v) comparison of trees constructed for multiple protein families. All constructed trees support the separation of the two primary prokaryotic domains, bacteria and archaea, as well as some terminal bifurcations within the bacterial and archaeal domains. Beyond these obvious groupings, the trees made with different methods appeared to differ substantially in terms of the relative contributions of phylogenetic relationships and similarities in gene repertoires caused by similar life styles and horizontal gene transfer to the tree topology. The trees based on presence-absence of genomes in orthologous clusters and the trees based on conserved gene pairs appear to be strongly affected by gene loss and horizontal gene transfer. The trees based on identity distributions for orthologs and particularly the tree made of concatenated ribosomal protein sequences seemed to carry a stronger phylogenetic signal. The latter tree supported three potential high-level bacterial clades,: i) Chlamydia-Spirochetes, ii) Thermotogales-Aquificales (bacterial hyperthermophiles), and ii) Actinomycetes-Deinococcales-Cyanobacteria. The latter group also appeared to join the low-GC Gram-positive bacteria at a deeper tree node. These new groupings of bacteria were supported by the analysis of alternative topologies in the concatenated ribosomal protein tree using the Kishino-Hasegawa test and by a census of the topologies of 132 individual groups of orthologous proteins. Additionally, the results of this analysis put into question the sister-group relationship between the two major archaeal groups, Euryarchaeota and Crenarchaeota, and suggest instead that Euryarchaeota might be a paraphyletic group with respect to Crenarchaeota.
Yuri I Wolf, Igor B Rogozin, Nick V Grishin, Roman L Tatusov, and Eugene V Koonin
Genome trees constructed using five different approaches suggest new major bacterial clades
BMC Evol Biol. 2001; 1: 8.
Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase.
The ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell.
An interesting finding was the grouping (albeit weak) of Nostoc muscorum and Synechosystis sp. with Deinococcus radiodurans to form a high level clade (Figure 1). This is similar to findings from genome trees that suggest a close relationship between the Cyanobacteria and Deinococcales [32], although our 16S rRNA tree does not suggest a relationship between these taxa and the Actinobacteria. However, the Actinobacteria (High GC Gram-positives) did clearly separate from the Low GC Gram-positive Bacteria (Figure 1).
... the arsC sequences from major divisions of Bacteria such as the Green Sulfur Bacteria (represented by Chlorobium tepidum) and the Deinococcales (represented by D. radiodurans) are loosely associated with either the Enterobacteriales/α-Proteobacteria (Figure 2) or Low GC Gram-positive Bacteria (Figure 3) depending upon the analysis used, but in either case diverge to form their own deep branches, suggesting that they possess distinct arsenate reductases.
The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today. Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT) in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution. Plasmid-borne arsC genes are not monophyletic suggesting multiple cases of chromosomal-plasmid exchange and subsequent HGT. Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.
Colin R Jackson and Sandra L Dugas. Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase. BMC Evol Biol. 2003; 3: 18.
>> Order Deinococcales > Genus Deinococcus
>> Order Thermales > Genus Thermus
Deinococcales Deinococcus
Thermales Thermus Meiothermus Marinithermus Oceanithermus Vulcanithermus
(tem Deinococcus radiodurans) Conan the Bacterium Metabolic pathways D. radiodurans
D. radiodurans
Phylogenetic diversity of the deinococci as determined by 16S ribosomal DNA sequence comparison
Genome trees constructed using five different approaches suggest new major bacterial clades.
Five largely independent approaches were employed to construct trees for completely sequenced bacterial and archaeal genomes: i) presence-absence of genomes in clusters of orthologous genes; ii) conservation of local gene order (gene pairs) among prokaryotic genomes; iii) parameters of identity distribution for probable orthologs; iv) analysis of concatenated alignments of ribosomal proteins; v) comparison of trees constructed for multiple protein families. All constructed trees support the separation of the two primary prokaryotic domains, bacteria and archaea, as well as some terminal bifurcations within the bacterial and archaeal domains. Beyond these obvious groupings, the trees made with different methods appeared to differ substantially in terms of the relative contributions of phylogenetic relationships and similarities in gene repertoires caused by similar life styles and horizontal gene transfer to the tree topology. The trees based on presence-absence of genomes in orthologous clusters and the trees based on conserved gene pairs appear to be strongly affected by gene loss and horizontal gene transfer. The trees based on identity distributions for orthologs and particularly the tree made of concatenated ribosomal protein sequences seemed to carry a stronger phylogenetic signal. The latter tree supported three potential high-level bacterial clades,: i) Chlamydia-Spirochetes, ii) Thermotogales-Aquificales (bacterial hyperthermophiles), and ii) Actinomycetes-Deinococcales-Cyanobacteria. The latter group also appeared to join the low-GC Gram-positive bacteria at a deeper tree node. These new groupings of bacteria were supported by the analysis of alternative topologies in the concatenated ribosomal protein tree using the Kishino-Hasegawa test and by a census of the topologies of 132 individual groups of orthologous proteins. Additionally, the results of this analysis put into question the sister-group relationship between the two major archaeal groups, Euryarchaeota and Crenarchaeota, and suggest instead that Euryarchaeota might be a paraphyletic group with respect to Crenarchaeota.
Yuri I Wolf, Igor B Rogozin, Nick V Grishin, Roman L Tatusov, and Eugene V Koonin
Genome trees constructed using five different approaches suggest new major bacterial clades
BMC Evol Biol. 2001; 1: 8.
Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase.
The ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell.
An interesting finding was the grouping (albeit weak) of Nostoc muscorum and Synechosystis sp. with Deinococcus radiodurans to form a high level clade (Figure 1). This is similar to findings from genome trees that suggest a close relationship between the Cyanobacteria and Deinococcales [32], although our 16S rRNA tree does not suggest a relationship between these taxa and the Actinobacteria. However, the Actinobacteria (High GC Gram-positives) did clearly separate from the Low GC Gram-positive Bacteria (Figure 1).
... the arsC sequences from major divisions of Bacteria such as the Green Sulfur Bacteria (represented by Chlorobium tepidum) and the Deinococcales (represented by D. radiodurans) are loosely associated with either the Enterobacteriales/α-Proteobacteria (Figure 2) or Low GC Gram-positive Bacteria (Figure 3) depending upon the analysis used, but in either case diverge to form their own deep branches, suggesting that they possess distinct arsenate reductases.
The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today. Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT) in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution. Plasmid-borne arsC genes are not monophyletic suggesting multiple cases of chromosomal-plasmid exchange and subsequent HGT. Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.
Colin R Jackson and Sandra L Dugas. Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase. BMC Evol Biol. 2003; 3: 18.
0 Glossary:
Post a Comment
<< Home