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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.


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a Structural overlap of the D2 protein of Photosystem II (gray) and the last five transmembrane helices of the PsaB subunit of Photosystem I (orange). The amino acids that are strictly conserved are shown in sticks, and the corresponding sequence numbers are given according to the crystal structures 3ARC (Photosystem II) and 1JB0 (Photosystem I). b Position of the special pair pigment PB and PD2 relative to the tenth and fourth transmembrane helices of PsaB and D2, respectively. The question mark highlights two residues that could be homologous but occupy different structural positions
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Fig8: a Structural overlap of the D2 protein of Photosystem II (gray) and the last five transmembrane helices of the PsaB subunit of Photosystem I (orange). The amino acids that are strictly conserved are shown in sticks, and the corresponding sequence numbers are given according to the crystal structures 3ARC (Photosystem II) and 1JB0 (Photosystem I). b Position of the special pair pigment PB and PD2 relative to the tenth and fourth transmembrane helices of PsaB and D2, respectively. The question mark highlights two residues that could be homologous but occupy different structural positions

Mentions: Robust structural and sequence alignments of Type I and Type II reaction center subunits are required in order to reconstruct the properties of the ancestral reaction center at the dawn of photosynthesis. However, a proper alignment of Type I and Type II reaction center subunit sequences is by no means trivial (Rutherford et al. 1996), and it is impossible to obtain using conventional alignment algorithms such as Clustal or Muscle, regardless of the parameters used or amino acid substitution models applied. Indeed, the original arguments for Type I and Type II sharing a common ancestor reaction center came from structural and functional similarities (Nitschke and Rutherford 1991; Rutherford et al. 1996). This is because the sequence identity preserved between the two types of reaction centers is at best 5 %; needless to say, numerous insertions and deletions have occurred across sequences and lineages obscuring any sign of sequence homology. An overlap of the 3D structure of the D2 subunit of Photosystem II with the reaction center domain of PsaB of Photosystem I shows only 13 possible strictly conserved amino acids between the two, from approximately 350 (Fig. 8a, also see Sadekar et al. (2006) for a detailed structural analysis). The structural overlap can be used as templates to align the sequences and verify homologous regions. This reveals a number of interesting aspects about the evolution of reaction centers and the changes that had to occur from an ancestral reaction center to generate the two distinct types known.Fig. 8


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

Cardona T - Photosyn. Res. (2014)

a Structural overlap of the D2 protein of Photosystem II (gray) and the last five transmembrane helices of the PsaB subunit of Photosystem I (orange). The amino acids that are strictly conserved are shown in sticks, and the corresponding sequence numbers are given according to the crystal structures 3ARC (Photosystem II) and 1JB0 (Photosystem I). b Position of the special pair pigment PB and PD2 relative to the tenth and fourth transmembrane helices of PsaB and D2, respectively. The question mark highlights two residues that could be homologous but occupy different structural positions
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4582080&req=5

Fig8: a Structural overlap of the D2 protein of Photosystem II (gray) and the last five transmembrane helices of the PsaB subunit of Photosystem I (orange). The amino acids that are strictly conserved are shown in sticks, and the corresponding sequence numbers are given according to the crystal structures 3ARC (Photosystem II) and 1JB0 (Photosystem I). b Position of the special pair pigment PB and PD2 relative to the tenth and fourth transmembrane helices of PsaB and D2, respectively. The question mark highlights two residues that could be homologous but occupy different structural positions
Mentions: Robust structural and sequence alignments of Type I and Type II reaction center subunits are required in order to reconstruct the properties of the ancestral reaction center at the dawn of photosynthesis. However, a proper alignment of Type I and Type II reaction center subunit sequences is by no means trivial (Rutherford et al. 1996), and it is impossible to obtain using conventional alignment algorithms such as Clustal or Muscle, regardless of the parameters used or amino acid substitution models applied. Indeed, the original arguments for Type I and Type II sharing a common ancestor reaction center came from structural and functional similarities (Nitschke and Rutherford 1991; Rutherford et al. 1996). This is because the sequence identity preserved between the two types of reaction centers is at best 5 %; needless to say, numerous insertions and deletions have occurred across sequences and lineages obscuring any sign of sequence homology. An overlap of the 3D structure of the D2 subunit of Photosystem II with the reaction center domain of PsaB of Photosystem I shows only 13 possible strictly conserved amino acids between the two, from approximately 350 (Fig. 8a, also see Sadekar et al. (2006) for a detailed structural analysis). The structural overlap can be used as templates to align the sequences and verify homologous regions. This reveals a number of interesting aspects about the evolution of reaction centers and the changes that had to occur from an ancestral reaction center to generate the two distinct types known.Fig. 8

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