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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

Evolutionary models depicting the positions of phyla with phototrophic bacteria. The tree shown in a was constructed by Segata et al. (2013) from hundreds of proteins and using thousands of genomes. The phylogenetic method, sequence alignments, and phylogenetic tree are freely available from the author’s website (http://huttenhower.sph.harvard.edu/phylophlan). The tree has been redrawn in here to highlight the relative positions of phyla with phototrophic bacteria. Notice the basal position of the Firmicutes, and the close relationships of the Cyanobacteria and the Chloroflexi, the Acidobacteria and the Proteobacteria, as well as the Chlorobi and the Gemmatimonadetes. b–d Schematic trees where all non-phototrophic clades have been omitted for simplicity. The tree in b is based on that reported by Ciccarelli et al. (2006), and the one in c is based on that reported by Battistuzzi and Hedges (2009). The tree in d is based on the work by Jun et al. (2010) and has a very similar branching pattern compared to that by Segata et al. (2013). However, while the latter is based on sequence alignments of protein sequences, the former was constructed using an alignment-free approach
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Fig9: Evolutionary models depicting the positions of phyla with phototrophic bacteria. The tree shown in a was constructed by Segata et al. (2013) from hundreds of proteins and using thousands of genomes. The phylogenetic method, sequence alignments, and phylogenetic tree are freely available from the author’s website (http://huttenhower.sph.harvard.edu/phylophlan). The tree has been redrawn in here to highlight the relative positions of phyla with phototrophic bacteria. Notice the basal position of the Firmicutes, and the close relationships of the Cyanobacteria and the Chloroflexi, the Acidobacteria and the Proteobacteria, as well as the Chlorobi and the Gemmatimonadetes. b–d Schematic trees where all non-phototrophic clades have been omitted for simplicity. The tree in b is based on that reported by Ciccarelli et al. (2006), and the one in c is based on that reported by Battistuzzi and Hedges (2009). The tree in d is based on the work by Jun et al. (2010) and has a very similar branching pattern compared to that by Segata et al. (2013). However, while the latter is based on sequence alignments of protein sequences, the former was constructed using an alignment-free approach

Mentions: Since the first molecular studies on the evolution of bacteria based on rRNA phylogenies (Woese 1987), our understanding of the relationships among the different bacteria groups has progressed enormously. Although many questions remain to be answered, a more consistent picture for the evolution of chlorophyll- and bacteriochlorophyll-based phototrophy is starting to emerge. Figure 9a shows a large phylogenetic tree for the evolution of prokaryotes constructed using >400 different proteins from among 3737 genomes (Segata et al. 2013). This tree includes for the first time sequences from all seven phyla known to contain phototrophic species. Figure 9b, c shows schematic representations of different phylogenetic trees constructed using very large datasets and different methodologies (Ciccarelli et al. 2006; Battistuzzi and Hedges 2009; Jun et al. 2010). Although they differ in a number of aspects, they have several important traits in common that are of relevance to understand the diversification of photochemical reaction centers.Fig. 9


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

Cardona T - Photosyn. Res. (2014)

Evolutionary models depicting the positions of phyla with phototrophic bacteria. The tree shown in a was constructed by Segata et al. (2013) from hundreds of proteins and using thousands of genomes. The phylogenetic method, sequence alignments, and phylogenetic tree are freely available from the author’s website (http://huttenhower.sph.harvard.edu/phylophlan). The tree has been redrawn in here to highlight the relative positions of phyla with phototrophic bacteria. Notice the basal position of the Firmicutes, and the close relationships of the Cyanobacteria and the Chloroflexi, the Acidobacteria and the Proteobacteria, as well as the Chlorobi and the Gemmatimonadetes. b–d Schematic trees where all non-phototrophic clades have been omitted for simplicity. The tree in b is based on that reported by Ciccarelli et al. (2006), and the one in c is based on that reported by Battistuzzi and Hedges (2009). The tree in d is based on the work by Jun et al. (2010) and has a very similar branching pattern compared to that by Segata et al. (2013). However, while the latter is based on sequence alignments of protein sequences, the former was constructed using an alignment-free approach
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig9: Evolutionary models depicting the positions of phyla with phototrophic bacteria. The tree shown in a was constructed by Segata et al. (2013) from hundreds of proteins and using thousands of genomes. The phylogenetic method, sequence alignments, and phylogenetic tree are freely available from the author’s website (http://huttenhower.sph.harvard.edu/phylophlan). The tree has been redrawn in here to highlight the relative positions of phyla with phototrophic bacteria. Notice the basal position of the Firmicutes, and the close relationships of the Cyanobacteria and the Chloroflexi, the Acidobacteria and the Proteobacteria, as well as the Chlorobi and the Gemmatimonadetes. b–d Schematic trees where all non-phototrophic clades have been omitted for simplicity. The tree in b is based on that reported by Ciccarelli et al. (2006), and the one in c is based on that reported by Battistuzzi and Hedges (2009). The tree in d is based on the work by Jun et al. (2010) and has a very similar branching pattern compared to that by Segata et al. (2013). However, while the latter is based on sequence alignments of protein sequences, the former was constructed using an alignment-free approach
Mentions: Since the first molecular studies on the evolution of bacteria based on rRNA phylogenies (Woese 1987), our understanding of the relationships among the different bacteria groups has progressed enormously. Although many questions remain to be answered, a more consistent picture for the evolution of chlorophyll- and bacteriochlorophyll-based phototrophy is starting to emerge. Figure 9a shows a large phylogenetic tree for the evolution of prokaryotes constructed using >400 different proteins from among 3737 genomes (Segata et al. 2013). This tree includes for the first time sequences from all seven phyla known to contain phototrophic species. Figure 9b, c shows schematic representations of different phylogenetic trees constructed using very large datasets and different methodologies (Ciccarelli et al. 2006; Battistuzzi and Hedges 2009; Jun et al. 2010). Although they differ in a number of aspects, they have several important traits in common that are of relevance to understand the diversification of photochemical reaction centers.Fig. 9

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