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A fresh look at the evolution and diversification of photochemical reaction centers.

Cardona T - Photosyn. Res. (2014)

Bottom Line: In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments.Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria.The primordial phototrophic ancestor must have had both Type I and Type II reaction centers.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. t.cardona@imperial.ac.uk.

ABSTRACT
In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers.

No MeSH data available.


Related in: MedlinePlus

Maximum likelihood phylogenetic tree of Type II reaction center subunits. At the top, the tree is shown as a rectangular phylogram, and the same tree is displayed at the bottom as a radial phylogram to highlight the different clades. Sequences were aligned with ClustalX 2.1 (Larkin et al. 2007), and homologous positions were confirmed by overlapping the crystal structures of B. viridis (2PRC) and T. vulcanus (3ARC). The tree was calculated using PhyML 3.1 (Guindon et al. 2010), using the LG model of amino acid substitution and four substitution rate categories. The branch support was calculated with the Approximate Likelihood-Ratio Test (Anisimova and Gascuel 2006). The equilibrium frequencies, proportion of invariable sites, and the gamma shape parameter were set to be calculated by the program. Sequence alignments are available on request
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Fig3: Maximum likelihood phylogenetic tree of Type II reaction center subunits. At the top, the tree is shown as a rectangular phylogram, and the same tree is displayed at the bottom as a radial phylogram to highlight the different clades. Sequences were aligned with ClustalX 2.1 (Larkin et al. 2007), and homologous positions were confirmed by overlapping the crystal structures of B. viridis (2PRC) and T. vulcanus (3ARC). The tree was calculated using PhyML 3.1 (Guindon et al. 2010), using the LG model of amino acid substitution and four substitution rate categories. The branch support was calculated with the Approximate Likelihood-Ratio Test (Anisimova and Gascuel 2006). The equilibrium frequencies, proportion of invariable sites, and the gamma shape parameter were set to be calculated by the program. Sequence alignments are available on request

Mentions: All Type II reaction center proteins share a common origin. Therefore, it is possible to reconstruct their evolutionary relationships based on sequence alignments and phylogenetic analysis. The maximum likelihood phylogenetic tree in Fig. 3 shows the known evolutionary relationships between Type II reaction center proteins. It has basically the same topology as trees reported before (Beanland 1990; Blankenship 1992), which were constructed with a limited sequence data set and using parsimony-based phylogenetics. Similar results were obtained using structure-based phylogenies and distance methods (Sadekar et al. 2006). The tree indicates that Cyanobacterial Photosystem II reaction center proteins, D1 and D2, share a common ancestor, while the subunits from anoxygenic reaction centers, L and M, share a different common ancestor forming a separate branch of the tree (Beanland 1990; Blankenship 1992). It can be deduced that Type II reaction centers passed through a homodimeric stage before the evolution of heterodimericity. In other words, the heterodimeric character of all known Type II reaction centers evolved twice after two separate gene duplication events: one that produced the precursor genes for the L and M subunit, and the other for the D1 and D2 subunits.Fig. 3


A fresh look at the evolution and diversification of photochemical reaction centers.

Cardona T - Photosyn. Res. (2014)

Maximum likelihood phylogenetic tree of Type II reaction center subunits. At the top, the tree is shown as a rectangular phylogram, and the same tree is displayed at the bottom as a radial phylogram to highlight the different clades. Sequences were aligned with ClustalX 2.1 (Larkin et al. 2007), and homologous positions were confirmed by overlapping the crystal structures of B. viridis (2PRC) and T. vulcanus (3ARC). The tree was calculated using PhyML 3.1 (Guindon et al. 2010), using the LG model of amino acid substitution and four substitution rate categories. The branch support was calculated with the Approximate Likelihood-Ratio Test (Anisimova and Gascuel 2006). The equilibrium frequencies, proportion of invariable sites, and the gamma shape parameter were set to be calculated by the program. Sequence alignments are available on request
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4582080&req=5

Fig3: Maximum likelihood phylogenetic tree of Type II reaction center subunits. At the top, the tree is shown as a rectangular phylogram, and the same tree is displayed at the bottom as a radial phylogram to highlight the different clades. Sequences were aligned with ClustalX 2.1 (Larkin et al. 2007), and homologous positions were confirmed by overlapping the crystal structures of B. viridis (2PRC) and T. vulcanus (3ARC). The tree was calculated using PhyML 3.1 (Guindon et al. 2010), using the LG model of amino acid substitution and four substitution rate categories. The branch support was calculated with the Approximate Likelihood-Ratio Test (Anisimova and Gascuel 2006). The equilibrium frequencies, proportion of invariable sites, and the gamma shape parameter were set to be calculated by the program. Sequence alignments are available on request
Mentions: All Type II reaction center proteins share a common origin. Therefore, it is possible to reconstruct their evolutionary relationships based on sequence alignments and phylogenetic analysis. The maximum likelihood phylogenetic tree in Fig. 3 shows the known evolutionary relationships between Type II reaction center proteins. It has basically the same topology as trees reported before (Beanland 1990; Blankenship 1992), which were constructed with a limited sequence data set and using parsimony-based phylogenetics. Similar results were obtained using structure-based phylogenies and distance methods (Sadekar et al. 2006). The tree indicates that Cyanobacterial Photosystem II reaction center proteins, D1 and D2, share a common ancestor, while the subunits from anoxygenic reaction centers, L and M, share a different common ancestor forming a separate branch of the tree (Beanland 1990; Blankenship 1992). It can be deduced that Type II reaction centers passed through a homodimeric stage before the evolution of heterodimericity. In other words, the heterodimeric character of all known Type II reaction centers evolved twice after two separate gene duplication events: one that produced the precursor genes for the L and M subunit, and the other for the D1 and D2 subunits.Fig. 3

Bottom Line: In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments.Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria.The primordial phototrophic ancestor must have had both Type I and Type II reaction centers.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. t.cardona@imperial.ac.uk.

ABSTRACT
In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers.

No MeSH data available.


Related in: MedlinePlus