Limits...
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

Sequence alignment of the L subunit from Roseiflexus spp. and the D1 subunit from T. elongatus. The alignment shows that the parallel alpha helix that in D1 is essential for the assembly and coordination of the Mn4CaO5 cluster a has sequence and structural homology to a putative sixth transmembrane helix predicted from the fused LM reaction center subunit in Roseiflexus (b). In bold colored letters, the conserved amino acids between the two Roseiflexus sequences and T. elongatus are highlighted. The colored letters that are not in bold show positive amino acid substitutions. The underline highlights the fifth transmembrane helix and the following alpha helix (parallel in D1 and transmembrane in L from Roseiflexus spp.). Sequences from a few phototrophic Chloroflexi and Proteobacteria strains are also shown. Surprisingly, the L subunit from the proteobacterium Roseivivax halodurans extends middle way through the predicted sixth helix. The black dots under the T. elongatus sequence are the ligands to the Mn4CaO5 cluster. a The transmembrane and parallel alpha helices of D1. b A homology model of the L subunit from Roseiflexus built using the subunit from B. viridis as a template. The model was made with the SWISS-MODEL automated service (Guex et al. 2009). The position of the putative sixth helix depicted in b is only hypothetical and just for illustration purposes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4582080&req=5

Fig6: Sequence alignment of the L subunit from Roseiflexus spp. and the D1 subunit from T. elongatus. The alignment shows that the parallel alpha helix that in D1 is essential for the assembly and coordination of the Mn4CaO5 cluster a has sequence and structural homology to a putative sixth transmembrane helix predicted from the fused LM reaction center subunit in Roseiflexus (b). In bold colored letters, the conserved amino acids between the two Roseiflexus sequences and T. elongatus are highlighted. The colored letters that are not in bold show positive amino acid substitutions. The underline highlights the fifth transmembrane helix and the following alpha helix (parallel in D1 and transmembrane in L from Roseiflexus spp.). Sequences from a few phototrophic Chloroflexi and Proteobacteria strains are also shown. Surprisingly, the L subunit from the proteobacterium Roseivivax halodurans extends middle way through the predicted sixth helix. The black dots under the T. elongatus sequence are the ligands to the Mn4CaO5 cluster. a The transmembrane and parallel alpha helices of D1. b A homology model of the L subunit from Roseiflexus built using the subunit from B. viridis as a template. The model was made with the SWISS-MODEL automated service (Guex et al. 2009). The position of the putative sixth helix depicted in b is only hypothetical and just for illustration purposes

Mentions: Although one protein is predicted from the gene sequence, isolation of the reaction center followed by denaturing SDS electrophoresis showed that the L and M subunits had been cleaved (Yamada et al. 2005; Collins et al. 2009), suggesting posttranslational processing of the original gene product at the C-terminus of the L subunit. In Photosystem II, a 9 to 16 amino acid extension at the C-terminus of the D1 protein is cleaved as part of the assembly process of the Photosystem II complex. This is required to allow full activation of the Mn4CaO5 cluster (Nixon et al. 1992), because the terminal carboxylate group of Ala344 provides a bidentate ligand to two of the Mn atoms (Umena et al. 2011). The posttranslational cleavage of the D1 protein and the cleavage of the pufLM gene product strike the author as too similar to be coincidental. To explore the possibility of an unexpected relationship between the Type II reaction center of Roseiflexus spp. and Photosystem II, and to try to understand the origin or role of the region between the L and M subunit, I took a closer look at the Roseiflexus spp. LM predicted sequence (see Fig. 6).Fig. 6


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

Cardona T - Photosyn. Res. (2014)

Sequence alignment of the L subunit from Roseiflexus spp. and the D1 subunit from T. elongatus. The alignment shows that the parallel alpha helix that in D1 is essential for the assembly and coordination of the Mn4CaO5 cluster a has sequence and structural homology to a putative sixth transmembrane helix predicted from the fused LM reaction center subunit in Roseiflexus (b). In bold colored letters, the conserved amino acids between the two Roseiflexus sequences and T. elongatus are highlighted. The colored letters that are not in bold show positive amino acid substitutions. The underline highlights the fifth transmembrane helix and the following alpha helix (parallel in D1 and transmembrane in L from Roseiflexus spp.). Sequences from a few phototrophic Chloroflexi and Proteobacteria strains are also shown. Surprisingly, the L subunit from the proteobacterium Roseivivax halodurans extends middle way through the predicted sixth helix. The black dots under the T. elongatus sequence are the ligands to the Mn4CaO5 cluster. a The transmembrane and parallel alpha helices of D1. b A homology model of the L subunit from Roseiflexus built using the subunit from B. viridis as a template. The model was made with the SWISS-MODEL automated service (Guex et al. 2009). The position of the putative sixth helix depicted in b is only hypothetical and just for illustration purposes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig6: Sequence alignment of the L subunit from Roseiflexus spp. and the D1 subunit from T. elongatus. The alignment shows that the parallel alpha helix that in D1 is essential for the assembly and coordination of the Mn4CaO5 cluster a has sequence and structural homology to a putative sixth transmembrane helix predicted from the fused LM reaction center subunit in Roseiflexus (b). In bold colored letters, the conserved amino acids between the two Roseiflexus sequences and T. elongatus are highlighted. The colored letters that are not in bold show positive amino acid substitutions. The underline highlights the fifth transmembrane helix and the following alpha helix (parallel in D1 and transmembrane in L from Roseiflexus spp.). Sequences from a few phototrophic Chloroflexi and Proteobacteria strains are also shown. Surprisingly, the L subunit from the proteobacterium Roseivivax halodurans extends middle way through the predicted sixth helix. The black dots under the T. elongatus sequence are the ligands to the Mn4CaO5 cluster. a The transmembrane and parallel alpha helices of D1. b A homology model of the L subunit from Roseiflexus built using the subunit from B. viridis as a template. The model was made with the SWISS-MODEL automated service (Guex et al. 2009). The position of the putative sixth helix depicted in b is only hypothetical and just for illustration purposes
Mentions: Although one protein is predicted from the gene sequence, isolation of the reaction center followed by denaturing SDS electrophoresis showed that the L and M subunits had been cleaved (Yamada et al. 2005; Collins et al. 2009), suggesting posttranslational processing of the original gene product at the C-terminus of the L subunit. In Photosystem II, a 9 to 16 amino acid extension at the C-terminus of the D1 protein is cleaved as part of the assembly process of the Photosystem II complex. This is required to allow full activation of the Mn4CaO5 cluster (Nixon et al. 1992), because the terminal carboxylate group of Ala344 provides a bidentate ligand to two of the Mn atoms (Umena et al. 2011). The posttranslational cleavage of the D1 protein and the cleavage of the pufLM gene product strike the author as too similar to be coincidental. To explore the possibility of an unexpected relationship between the Type II reaction center of Roseiflexus spp. and Photosystem II, and to try to understand the origin or role of the region between the L and M subunit, I took a closer look at the Roseiflexus spp. LM predicted sequence (see Fig. 6).Fig. 6

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