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Molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen IX.

Kobayashi K, Masuda T, Tajima N, Wada H, Sato N - Genome Biol Evol (2014)

Bottom Line: Land plants have a unique HemY homolog that is also shared by Chloroflexus species, in addition to the main HemY homolog originating from Cyanobacteria.Meanwhile, organisms missing any Protox can be classified into two groups; those lacking most heme synthetic genes, which necessarily depend on external heme supply, and those lacking only genes involved in the conversion of uroporphyrinogen III into heme, which would use a precorrin2-dependent alternative pathway.However, hemN encoding coproporphyrinogen IX oxidase was frequently found in organisms lacking Protox enzyme, which suggests a unique role of this gene other than in heme biosynthesis.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan kkobayashi@bio.c.u-tokyo.ac.jp naokisat@bio.c.u-tokyo.ac.jp.

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Phylogenic trees used for AU testing. Twenty representative HemY proteins were selected, and the most likely trees were evaluated by AU test. Trees 1–15 were selected by the protml program. Trees 16–19 were tested as constrained trees. The results of the AU test are in table 3. Both JTT and WAG models were tested. Trees 1–15 should not be rejected as nonsignificant, whereas trees 16–19 were clearly abandoned. For names of eukaryotes, see table 1. Other names are the followings: Bsu, Bacillus subtilis; Caur, Chloroflexus aurantiacus; Fal, Frankia alni; Glv, Gloeobacter violaceus; Roca, Roseiflexus castenholzii; Sthe, Sphaerobacter thermophilus; Tel, Thermosynechococcus elongatus; Ter, Trichodesmium erythraeum; Tth, Thermus thermophilus; YelA, Cyanobacterium Yellowstone A-prime.
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evu170-F5: Phylogenic trees used for AU testing. Twenty representative HemY proteins were selected, and the most likely trees were evaluated by AU test. Trees 1–15 were selected by the protml program. Trees 16–19 were tested as constrained trees. The results of the AU test are in table 3. Both JTT and WAG models were tested. Trees 1–15 should not be rejected as nonsignificant, whereas trees 16–19 were clearly abandoned. For names of eukaryotes, see table 1. Other names are the followings: Bsu, Bacillus subtilis; Caur, Chloroflexus aurantiacus; Fal, Frankia alni; Glv, Gloeobacter violaceus; Roca, Roseiflexus castenholzii; Sthe, Sphaerobacter thermophilus; Tel, Thermosynechococcus elongatus; Ter, Trichodesmium erythraeum; Tth, Thermus thermophilus; YelA, Cyanobacterium Yellowstone A-prime.

Mentions: HemYs from Chloroflexus aurantiacus and Chloroflexus aggregans branch from the root of the plant PPO2 clade (fig. 4). The HemY sequences from other Chloroflexi such as Roseiflexus species belong to a large bacterial clade with those from Actinobacteria and Firmicutes. To ascertain this result, we performed the AU test for 19 phylogenic trees constructed from 20 representative taxa (fig. 5 and table 3). All 15 trees in which the Chloroflexus hemY and plant PPO2 sequences formed sister branches (trees 1–15) gave AU probabilities >0.2 and therefore were not discarded. In contrast, trees in which the Chloroflexus HemY was placed on the bacterial branch (trees 16 and 17) or on the cyanobacterial branch (trees 18 and 19) gave AU values <0.05, which are sufficiently low to reject these possibilities. These data confirm that Chloroflexus HemY and plant PPO2 sequences form a branch separate from the branches of plant PPO1 and bacterial HemY.Fig. 5.—


Molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen IX.

Kobayashi K, Masuda T, Tajima N, Wada H, Sato N - Genome Biol Evol (2014)

Phylogenic trees used for AU testing. Twenty representative HemY proteins were selected, and the most likely trees were evaluated by AU test. Trees 1–15 were selected by the protml program. Trees 16–19 were tested as constrained trees. The results of the AU test are in table 3. Both JTT and WAG models were tested. Trees 1–15 should not be rejected as nonsignificant, whereas trees 16–19 were clearly abandoned. For names of eukaryotes, see table 1. Other names are the followings: Bsu, Bacillus subtilis; Caur, Chloroflexus aurantiacus; Fal, Frankia alni; Glv, Gloeobacter violaceus; Roca, Roseiflexus castenholzii; Sthe, Sphaerobacter thermophilus; Tel, Thermosynechococcus elongatus; Ter, Trichodesmium erythraeum; Tth, Thermus thermophilus; YelA, Cyanobacterium Yellowstone A-prime.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4231631&req=5

evu170-F5: Phylogenic trees used for AU testing. Twenty representative HemY proteins were selected, and the most likely trees were evaluated by AU test. Trees 1–15 were selected by the protml program. Trees 16–19 were tested as constrained trees. The results of the AU test are in table 3. Both JTT and WAG models were tested. Trees 1–15 should not be rejected as nonsignificant, whereas trees 16–19 were clearly abandoned. For names of eukaryotes, see table 1. Other names are the followings: Bsu, Bacillus subtilis; Caur, Chloroflexus aurantiacus; Fal, Frankia alni; Glv, Gloeobacter violaceus; Roca, Roseiflexus castenholzii; Sthe, Sphaerobacter thermophilus; Tel, Thermosynechococcus elongatus; Ter, Trichodesmium erythraeum; Tth, Thermus thermophilus; YelA, Cyanobacterium Yellowstone A-prime.
Mentions: HemYs from Chloroflexus aurantiacus and Chloroflexus aggregans branch from the root of the plant PPO2 clade (fig. 4). The HemY sequences from other Chloroflexi such as Roseiflexus species belong to a large bacterial clade with those from Actinobacteria and Firmicutes. To ascertain this result, we performed the AU test for 19 phylogenic trees constructed from 20 representative taxa (fig. 5 and table 3). All 15 trees in which the Chloroflexus hemY and plant PPO2 sequences formed sister branches (trees 1–15) gave AU probabilities >0.2 and therefore were not discarded. In contrast, trees in which the Chloroflexus HemY was placed on the bacterial branch (trees 16 and 17) or on the cyanobacterial branch (trees 18 and 19) gave AU values <0.05, which are sufficiently low to reject these possibilities. These data confirm that Chloroflexus HemY and plant PPO2 sequences form a branch separate from the branches of plant PPO1 and bacterial HemY.Fig. 5.—

Bottom Line: Land plants have a unique HemY homolog that is also shared by Chloroflexus species, in addition to the main HemY homolog originating from Cyanobacteria.Meanwhile, organisms missing any Protox can be classified into two groups; those lacking most heme synthetic genes, which necessarily depend on external heme supply, and those lacking only genes involved in the conversion of uroporphyrinogen III into heme, which would use a precorrin2-dependent alternative pathway.However, hemN encoding coproporphyrinogen IX oxidase was frequently found in organisms lacking Protox enzyme, which suggests a unique role of this gene other than in heme biosynthesis.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan kkobayashi@bio.c.u-tokyo.ac.jp naokisat@bio.c.u-tokyo.ac.jp.

Show MeSH
Related in: MedlinePlus