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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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Synteny in the hemG/hemJ replacement region in Prochlorococcus. (A) A 16S–23S-based phylogenetic tree of the Synechococcus–Prochlorococcus lineage along with deeply branched Gloeobacter violaceus. (B) Arrangement of genes in the regions containing hemG or hemJ in related Prochlorococcus strains.
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evu170-F2: Synteny in the hemG/hemJ replacement region in Prochlorococcus. (A) A 16S–23S-based phylogenetic tree of the Synechococcus–Prochlorococcus lineage along with deeply branched Gloeobacter violaceus. (B) Arrangement of genes in the regions containing hemG or hemJ in related Prochlorococcus strains.

Mentions: Each alignment was used in the phylogenetic analysis as follows. A neighbor-joining (NJ) tree was estimated with MEGA v4 (Tamura et al. 2007) with the Jones–Taylor–Thorton (JTT) model and an equal evolutionary rate. Calculation with the ML method involved use of TreeFinder March 2008 version (Jobb et al. 2004) with the Whelan–Goldman (WAG) model, and with RAxML v7.0.4 (Stamatakis 2006) with –f d –i 10 –m PROTCATWAG options. The exact parameters were determined by initial trials with –c 10, 40, 55 with or without –i 10. Bootstrap was based on 1,000 replicates. Bayesian inference (BI) involved use of MrBayes v3.2 (Ronquist and Huelsenbeck 2003), with the following options: aamodelpr = fixed(wag), ratepr = variable, ngen = 2,000,000, samplefreq = 200, burnin = 3,000 (for HemG, ngen = 1,000,000, samplefreq = 100), and with PhyloBayes v3.2e (Lartillot et al. 2009) with the CAT+gtr model. A 16S–23S-based phylogenetic tree in Cyanobacteria (fig. 2) was constructed with the BI method as described (Sasaki and Sato 2010).


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)

Synteny in the hemG/hemJ replacement region in Prochlorococcus. (A) A 16S–23S-based phylogenetic tree of the Synechococcus–Prochlorococcus lineage along with deeply branched Gloeobacter violaceus. (B) Arrangement of genes in the regions containing hemG or hemJ in related Prochlorococcus strains.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu170-F2: Synteny in the hemG/hemJ replacement region in Prochlorococcus. (A) A 16S–23S-based phylogenetic tree of the Synechococcus–Prochlorococcus lineage along with deeply branched Gloeobacter violaceus. (B) Arrangement of genes in the regions containing hemG or hemJ in related Prochlorococcus strains.
Mentions: Each alignment was used in the phylogenetic analysis as follows. A neighbor-joining (NJ) tree was estimated with MEGA v4 (Tamura et al. 2007) with the Jones–Taylor–Thorton (JTT) model and an equal evolutionary rate. Calculation with the ML method involved use of TreeFinder March 2008 version (Jobb et al. 2004) with the Whelan–Goldman (WAG) model, and with RAxML v7.0.4 (Stamatakis 2006) with –f d –i 10 –m PROTCATWAG options. The exact parameters were determined by initial trials with –c 10, 40, 55 with or without –i 10. Bootstrap was based on 1,000 replicates. Bayesian inference (BI) involved use of MrBayes v3.2 (Ronquist and Huelsenbeck 2003), with the following options: aamodelpr = fixed(wag), ratepr = variable, ngen = 2,000,000, samplefreq = 200, burnin = 3,000 (for HemG, ngen = 1,000,000, samplefreq = 100), and with PhyloBayes v3.2e (Lartillot et al. 2009) with the CAT+gtr model. A 16S–23S-based phylogenetic tree in Cyanobacteria (fig. 2) was constructed with the BI method as described (Sasaki and Sato 2010).

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