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

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

Probing the quinone binding site of Photosystem II from Thermosynechococcus elongatus containing either PsbA1 or PsbA3 as the D1 protein through the binding characteristics of herbicides

The main cofactors involved in Photosystem II (PSII) oxygen evolution activity are borne by two proteins, D1 (PsbA) and D2 (PsbD). In Thermosynechococcus elongatus, a thermophilic cyanobacterium, the D1 protein is predominantly encoded by either the psbA(1) or the psbA(3) gene, the expression of which depends on the environmental conditions. In this work, the Q(B) site properties in PsbA1-PSII and PsbA3-PSII were probed through the binding properties of DCMU, a urea-type herbicide, and bromoxynil, a phenolic-type herbicide. This was done by using helium temperature EPR spectroscopy and by monitoring the time-resolved changes of the redox state of Q(A) by absorption spectroscopy in PSII purified from a His(6)-tagged WT strain expressing PsbA1 or from a His(6)-tagged strain in which both the psbA(1) and psbA(2) genes have been deleted and which therefore only express PsbA3. It is shown that, in both PsbA1-PSII and PsbA3-PSII, bromoxynil does not bind to PSII when Q(B) is in its semiquinone state which indicates a much lower affinity for PSII when Q(A) is in its semiquinone state than when it is in its oxidized state. This is consistent with the midpoint potential of Q(A)(center dot-)/Q(A) being more negative in the presence of bromoxynil than in its absence [Krieger-Liszkay and Rutherford, Biochemistry 37 (1998) 17339-17344]. The addition in the dark of DCMU, but not that of bromoxynil, to PSII with a secondary electron acceptor in the Q(B)(center dot-) state induces the oxidation of the non-heme iron in a fraction of PsbA3-PSII but not in PsbA1-PSII. These results are explained as follows: i) bromoxynil has a lower affinity for PSII with the non-heme iron oxidized than DCMU therefore, ii) the midpoint potential of the Fe(II)/Fe(III) couple is lower with DCMU bound than with bromoxynil bound in PsbA3-PSII; and iii) the midpoint potential of the Fe(II)/Fe(III) couple is higher in PsbA1-PSII than in PsbA3-PSII. The observation of DCMU-induced oxidation of the non-heme iron leads us to propose that Q(2), an electron acceptor identified by Joliot and Joliot [FEBS Lett 134 (1981) 155-158], is the non-heme iron

Electronic structure of the oxygen-evolving complex in photosystem II prior to O-O bond formation

The photosynthetic protein complex photosystem II oxidizes water to molecular oxygen at an embedded tetramanganese-calcium cluster. Resolving the geometric and electronic structure of this cluster in its highest metastable catalytic state (designated S3) is a prerequisite for understanding the mechanism of O-O bond formation. Here, multifrequency, multidimensional magnetic resonance spectroscopy reveals that all four manganese ions of the catalyst are structurally and electronically similar immediately before the final oxygen evolution step; they all exhibit a 4+ formal oxidation state and octahedral local geometry. Only one structural model derived from quantum chemical modeling is consistent with all magnetic resonance data; its formation requires the binding of an additional water molecule. O-O bond formation would then proceed by the coupling of two proximal manganese-bound oxygens in the transition state of the cofactor

Detection of the Water-Binding Sites of the Oxygen-Evolving Complex of Photosystem II Using W-Band ¹⁷O Electron–Electron Double Resonance-Detected NMR Spectroscopy

Water binding to the Mn4O5Ca cluster of the oxygen-evolving complex (OEC) of Photosystem II (PSII) poised in the S2 state was studied via H217O- and 2H2O-labeling and high-field electron paramagnetic resonance (EPR) spectroscopy. Hyperfine couplings of coordinating 17O (I = 5/2) nuclei were detected using W-band (94 GHz) electron–electron double resonance (ELDOR) detected NMR and Davies/Mims electron–nuclear double resonance (ENDOR) techniques. Universal 15N (I = 1/2) labeling was employed to clearly discriminate the 17O hyperfine couplings that overlap with 14N (I = 1) signals from the D1-His332 ligand of the OEC (Stich Biochemistry 2011, 50 (34), 7390−7404). Three classes of 17O nuclei were identified: (i) one μ-oxo bridge; (ii) a terminal Mn–OH/OH2 ligand; and (iii) Mn/Ca–H2O ligand(s). These assignments are based on 17O model complex data, on comparison to the recent 1.9 Å resolution PSII crystal structure (Umena Nature 2011, 473, 55−60), on NH3 perturbation of the 17O signal envelope and density functional theory calculations. The relative orientation of the putative 17O μ-oxo bridge hyperfine tensor to the 14N(15N) hyperfine tensor of the D1-His332 ligand suggests that the exchangeable μ-oxo bridge links the outer Mn to the Mn3O3Ca open-cuboidal unit (O4 and O5 in the Umena et al. structure). Comparison to literature data favors the Ca-linked O5 oxygen over the alternative assignment to O4. All 17O signals were seen even after very short (≤15 s) incubations in H217O suggesting that all exchange sites identified could represent bound substrate in the S1 state including the μ-oxo bridge. 1H/2H (I = 1/2, 1) ENDOR data performed at Q- (34 GHz) and W-bands complement the above findings. The relatively small 1H/2H couplings observed require that all the μ-oxo bridges of the Mn4O5Ca cluster are deprotonated in the S2 state. Together, these results further limit the possible substrate water-binding sites and modes within the OEC. This information restricts the number of possible reaction pathways for O–O bond formation, supporting an oxo/oxyl coupling mechanism in S4