Architecture of the photosynthetic oxygen-evolving center

Fate of carotenoids in yeasts: synthesis and cleavage

Carotenoids and their cleavage products (norisoprenoids) have excellent functional properties with diverse applications in foods, medicaments, cosmetics, etc. Carotenoids can be oxidatively cleaved through nonspecific reactions or by carotenoid cleavage oxygenases (CCOs), the product of which could further modify food flavor. This review provides comprehensive information on both carotenoid synthesis and cleavage processes with emphasis on enzyme characterization and biosynthetic pathway optimization. The use of interdisciplinary approaches of bioengineering and computer-aided experimental technology for key enzyme modification and systematic pathway design is beneficial to monitor metabolic pathways and assess pathway bottlenecks, which could efficiently lead to accumulation of carotenoids in microorganisms. The identification of CCOs spatial structures isolated from different species has made a significant contribution to the current state of knowledge. Current trends in carotenoid-related flavor modification are also discussed. In particular, we propose the carotenoid-synthesizing yeast Rhodotorula spp. for the production of food bioactive compounds. Understanding the behavior underlying the formation of norisoprenoids from carotenoids using interdisciplinary approaches may point toward other areas of investigation that could lead to better exploiting the potential use of autochthonous yeast in flavor enhancement.

Homogeneous Water Oxidation Catalyzed by First-Row Transition Metal Complexes: Unveiling the Relationship between Turnover Frequency and Reaction Overpotential

The utilization of earth-abundant low-toxicity metal ions in the construction of highly active and efficient molecular catalysts promoting the water oxidation reaction is important for developing a sustainable artificial energy cycle. However, the kinetic and thermodynamic properties of the currently available molecular water oxidation catalysts (MWOCs) have not been comprehensively investigated. This Review summarizes the current status of MWOCs based on first-row transition metals in terms of their turnover frequency (TOF, a kinetic property) and overpotential (η, a thermodynamic property) and uses the relationship between log(TOF) and η to assess catalytic performance. Furthermore, the effects of the same ligand classes on these MWOCs are discussed in terms of TOF and η, and vice versa. The collective analysis of these relationships provides a metric for the direct comparison of catalyst systems and identifying factors crucial for catalyst design.

Material Evolution with Nanotechnology, Nanoarchitectonics, and Materials Informatics: What will be the Next Paradigm Shift in Nanoporous Materials?

Materials science and chemistry have played a central and significant role in advancing society. With the shift toward sustainable living, it is anticipated that the development of functional materials will continue to be vital for sustaining life on our planet. In the recent decades, rapid progress has been made in materials science and chemistry owing to the advances in experimental, analytical, and computational methods, thereby producing several novel and useful materials. However, most problems in material development are highly complex. Here, the best strategy for the development of functional materials via the implementation of three key concepts is discussed: nanotechnology as a game changer, nanoarchitectonics as an integrator, and materials informatics as a super-accelerator. Discussions from conceptual viewpoints and example recent developments, chiefly focused on nanoporous materials, are presented. It is anticipated that coupling these three strategies together will open advanced routes for the swift design and exploratory search of functional materials truly useful for solving real-world problems. These novel strategies will result in the evolution of nanoporous functional materials.

Electron transfer-triggered imaging of EGFR signaling activity

In vivo electron transfer processes are closely related to the activation of signaling pathways, and, thus, affect various life processes. Indeed, the signaling pathway activation of key molecules may be associated with certain diseases. For example, epidermal growth factor receptor (EGFR) activation is related to the occurrence and development of tumors. Hence, monitoring the activation of EGFR-related signaling pathways can help reveal the progression of tumor development. However, it is challenging for current detection methods to monitor the activation of specific signaling pathways in complex biochemical reactions. Here we designed a highly sensitive and specific nanoprobe that enables in vivo imaging of electronic transfer over a broad range of spatial and temporal scales. By using the ferrocene-DNA polymer “wire”, the electrons transferred in a biochemical reaction can flow to persistent luminescent nanoparticles and change their electron distribution, thereby altering the optical signal of the particles. This electron transfer-triggered imaging probe enables mapping the activation of EGFR-related signaling pathways in a temporally and spatially precise manner. By offering precise visualization of signaling activity, this approach may offer a general platform not only for understanding molecular mechanisms in various biological processes but also for promoting disease therapies and drug evaluation.

Here, the authors design a nanoprobe for in vivo imaging of electronic transfer, consisting of a ferrocene-DNA polymer to transfer electrons to luminescent nanoparticles, changing their optical signal. Using this probe, they map activation of EGFR signalling during tumour treatment.

Multiple Proton-Coupled Electron Transfers at a Tricopper Cluster: Modeling the Reductive Regeneration Process in Multicopper Oxidases

Metal clusters in enzymes carry out the life-sustaining reactions by accumulating multiple redox equivalents in a narrow potential range. This redox potential leveling effect commonly observed in Nature has yet to be reproduced with synthetic metal clusters. Herein, we employ a fully encapsulated synthetic tricopper complex to model the three-electron two-proton reductive regeneration of fully reduced trinuclear copper cluster Cu^ICu^ICu^I(μ₂-OH₂) (FR) from native intermediate Cu^IICu^IICu^II(μ₃-O) (NI) in multicopper oxidases (MCOs). The tricopper cluster can access four oxidation states (I,I,I to II,II,II) and four protonation states ([Cu₃(μ₃-O)]LH, [Cu₃(μ₃-OH)]L, [Cu₃(μ₃-OH)]LH, and [Cu₃(μ₃-OH₂)]L, where LH denotes the protonated ligand), allowing mechanistic investigation of proton-coupled electron transfer (PCET) relevant to MCOs. Seven tricopper complexes with discrete oxidation and protonation states were characterized with spectroscopy or X-ray single-crystal diffraction. A stepwise electron transfer-proton transfer (ET-PT) mechanism is established for the reduction of Cu^IICu^IICu^II(μ₃-O)LH to Cu^IICu^IICu^I(μ₃-OH)L, while a stepwise PT-ET mechanism is determined for the reduction of Cu^IICu^ICu^I(μ₃-OH)LH to Cu^ICu^ICu^I(μ₂-OH₂)L. The switch-over from ET-PT to PT-ET mechanism showcases that the tricopper complex can adopt different PCET mechanisms to circumvent high-barrier proton transfer steps. Overall, three-electron two-proton reduction occurs within a narrow potential range of 170 mV, exemplifying the redox potential leveling effect of secondary proton relays in delivering multiple redox equivalents at metal clusters.

Comparative chloroplast genome analyses of Paraboea (Gesneriaceae): Insights into adaptive evolution and phylogenetic analysis

Paraboea (Gesneriaceae) distributed in the karst areas of South and Southwest China and Southeast Asia, is an ideal genus to study the phylogeny and adaptive evolution of karst plants. In this study, the complete chloroplast genomes of twelve Paraboea species were sequenced and analyzed. Twelve chloroplast genomes ranged in size from 153166 to 154245 bp. Each chloroplast genome had a typical quartile structure, and relatively conserved type and number of gene components, including 131 genes which are composed of 87 protein coding genes, 36 transfer RNAs and 8 ribosomal RNAs. A total of 600 simple sequence repeats and 389 non-overlapped sequence repeats were obtained from the twelve Paraboea chloroplast genomes. We found ten divergent regions (trnH-GUG-psbA, trnM-CAU, trnC-GCA, atpF-atpH, ycf1, trnK-UUU-rps16, rps15, petL, trnS-GCU-trnR-UCU and psaJ-rpl33) among the 12 Paraboea species to be potential molecular markers. In the phylogenetic tree of 31 Gesneriaceae plants including twelve Paraboea species, all Paraboea species clustered in a clade and confirmed the monophyly of Paraboea. Nine genes with positive selection sites were detected, most of which were related to photosynthesis and protein synthesis, and might played crucial roles in the adaptability of Paraboea to diverse karst environments. These findings are valuable for further study of the phylogeny and karst adaptability of Gesneriaceae plants.

Synergistic effects of CH3CO2H and Ca2+ on C–H bond activation by MnO4−

The activation of metal-oxo species with Lewis acids is of current interest. In this work, the effects of a weak Brønsted acid such as CH₃CO₂H and a weak Lewis acid such as Ca²⁺ on C–H bond activation by KMnO₄ have been investigated. Although MnO₄⁻ is rather non-basic (pK_a of MnO₃(OH) = −2.25), it can be activated by AcOH or Ca²⁺ to oxidize cyclohexane at room temperature to give cyclohexanone as the major product. A synergistic effect occurs when both AcOH and Ca²⁺ are present; the relative rates for the oxidation of cyclohexane by MnO₄⁻/AcOH, MnO₄⁻/Ca²⁺ and MnO₄⁻/AcOH/Ca²⁺ are 1 : 73 : 198. DFT calculations show that in the active intermediate of MnO₄⁻/AcOH/Ca²⁺, MnO₄⁻ is H-bonded to 3 AcOH molecules, while Ca²⁺ is bonded to 3 AcOH molecules as well as to an oxo ligand of MnO₄⁻. Our results also suggest that these synergistic activating effects of a weak Brønsted acid and a weak Lewis acid should be applicable to a variety of metal-oxo species.

The activation of metal-oxo species with Lewis acids is of current interest.

Nitric oxide represses photosystem II and NDH-1 in the cyanobacterium Synechocystis sp. PCC 6803

Photosynthetic electron transfer comprises a series of light-induced redox reactions catalysed by multiprotein machinery in the thylakoid. These protein complexes possess cofactors susceptible to redox modifications by reactive small molecules. The gaseous radical nitric oxide (NO), a key signalling molecule in green algae and plants, has earlier been shown to bind to Photosystem (PS) II and obstruct electron transfer in plants. The effects of NO on cyanobacterial bioenergetics however, have long remained obscure. In this study, we exposed the model cyanobacterium Synechocystis sp. PCC 6803 to NO under anoxic conditions and followed changes in whole-cell fluorescence and oxidoreduction of P700 in vivo. Our results demonstrate that NO blocks photosynthetic electron transfer in cells by repressing PSII, PSI, and likely the NDH dehydrogenase-like complex 1 (NDH-1). We propose that iron‑sulfur clusters of NDH-1 complex may be affected by NO to such an extent that ferredoxin-derived electron injection to the plastoquinone pool, and thus cyclic electron transfer, may be inhibited. These findings reveal the profound effects of NO on Synechocystis cells and demonstrate the importance of controlled NO homeostasis in cyanobacteria.

The PsbJ protein is required for photosystem II activity in centers lacking the PsbO and PsbV lumenal subunits

Photosystem II (PS II) of oxygenic photosynthesis is found in the thylakoid membranes of plastids and cyanobacteria. The mature PS II complex comprises a central core of four membrane proteins that bind the majority of the redox-active cofactors. In cyanobacteria the central core is surrounded by 13 low-molecular-weight (LMW) subunits which each consist of one or two transmembrane helices. Three additional hydrophilic subunits known as PsbO, PsbU and PsbV are found associated with hydrophilic loops belonging to the core proteins protruding into the thylakoid lumen. During biogenesis the majority of the LMW subunits are known to initially associate with individual pre-assembly complexes consisting of one or more of the core proteins; however, the point at which the PsbJ LMW subunit binds to PS II is not known. The majority of models for PS II biogenesis propose that the three extrinsic proteins and PsbJ bind in the final stages of PS II assembly. We have investigated the impact of creating the double mutants ∆PsbJ:∆PsbO, ∆PsbJ:∆PsbU and ∆PsbJ:∆PsbV to investigate potential cooperation between these subunits in the final stages of biogenesis. Our results indicate that PsbJ can bind to PS II in the absence of any one of the extrinsic proteins. However, unlike their respective single mutants, the ∆PsbJ:∆PsbO and ∆PsbJ:∆PsbV strains were not photoautotrophic and were unable to support oxygen evolution suggesting a functional oxygen-evolving complex could not assemble in these strains. In contrast, the PS II centers formed in the ∆PsbJ:∆PsbU strain were capable of photoautotrophic growth and could support oxygen evolution when whole-chain electron transport was supported by the addition of bicarbonate.

Structural and dynamic insights into Mn4Ca cluster-depleted Photosystem II

In the first steps of natural oxygenic photosynthesis, sunlight is used to oxidize water molecules to protons, electrons and molecular oxygen. This reaction takes place on the Mn₄Ca cluster located in the reaction centre of Photosystem II (PSII), where the cluster is assembled and continuously repaired through a process known as photoactivation. Understanding the molecular details of such a process has important implications in different fields, in particular inspiring synthesis and repair strategies for artificial photosynthesis devices. In this regard, a detailed structural and dynamic characterization of Photosystem II lacking a Mn₄Ca cluster, namely apo PSII, is a prerequisite for the full comprehension of the photoactivation. Recently, the structure of the apo PSII was resolved at 2.55 Å resolution [Zhang et al., eLife, 2017, 6, e26933], suggesting a pre-organized structure of the protein cavity hosting the cluster. Anyway, the question of whether these findings are a feature of the method used remains open. Here, by means of classical Molecular Dynamics simulations, we characterized the structural and dynamic features of the apo PSII for different protonation states of the cluster cavity. Albeit an overall conformational stability common to all investigated systems, we found significant deviations in the conformation of the side chains of the active site with respect to the X-ray positions. Our findings suggest that not all residues acting as Mn ligands are pre-organized prior to the Mn₄Ca formation and previous local conformational changes are required in order to bind the first Mn ion in the high-affinity binding site.

Oxidation state variation in bis-calix[4]arene supported decametallic Mn clusters

The reaction of MnCl₂·4H₂O, H₈L (2,2'-bis-p-^tBu-calix[4]arene) and NEt₃ in a dmf/MeOH solvent mixture results in the formation of a mixed valent decametallic cluster of formula [MnII6MnIII4(L)₂(μ₃-OH)₄(μ-OH)₄(MeOH)₄(dmf)₄(MeCN)₂]·MeCN (3). Complex 3 crystallises in the monoclinic space group P2₁/n with the asymmetric unit comprising half of the compound. Structure solution reveals that the bis-calix[4]arene ligands are arranged such that one TBC[4] moiety in each has undergone inversion in order to accommodate a [MnIII4MnII6] metallic skeleton that describes three vertex-sharing [MnIII2MnII2] butterflies. The structure is closely related to the species [MnIII6MnII4(L)₂(μ₃-O)₂(μ₃-OH)₂(μ-OMe)₄(H₂O)₄(dmf)₈]·4dmf (4), the major difference being the oxidation level of the Mn ions in the core of the compound. DFT calculations on the full structures reveal that replacing the Mn^III ions in 4 for Mn^II ions in 3 results in a significant decrease in the magnitude of some antiferromagnetic exchange contributions, a switch from ferromagnetic to antiferromagnetic in others, and the loss of significant spin frustration.

Structure-based ligand design and discovery of novel tenuazonic acid derivatives with high herbicidal activity

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The model of lead molecule TeA binding to the QB site in Arabidopsis D1 protein was constructed.

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A series of new derivatives were designed and docked to the Q_B site of by molecular simulations.

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Derivatives D6, D13 and D27 with better affinities than TeA were screened out and synthesized.

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D6 and D13 are promising compounds to develop new PSII herbicides with superior performance.

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Model-based ligand design is a valuable tool to find new PSII inhibitors based on lead molecule TeA.

Introduction

Objectives

Methods

Results

Conclusion

Bioinspired Trinuclear Copper Catalyst for Water Oxidation with a Turnover Frequency up to 20000 s-1

Solar-powered water splitting is a dream reaction for constructing an artificial photosynthetic system for producing solar fuels. Natural photosystem II is a prototype template for research on artificial solar energy conversion by oxidizing water into molecular oxygen and supplying four electrons for fuel production. Although a range of synthetic molecular water oxidation catalysts have been developed, the understanding of O-O bond formation in this multielectron and multiproton catalytic process is limited, and thus water oxidation is still a big challenge. Herein, we report a trinuclear copper cluster that displays outstanding reactivity toward catalytic water oxidation inspired by multicopper oxidases (MCOs), which provides efficient catalytic four-electron reduction of O₂ to water. This synthetic mimic exhibits a turnover frequency of 20000 s^-1 in sodium bicarbonate solution, which is about 150 and 15 times higher than that of the mononuclear Cu catalyst (F-N₂O₂Cu, 131.6 s^-1) and binuclear Cu₂ complex (HappCu₂, 1375 s^-1), respectively. This work shows that the cooperation between multiple metals is an effective strategy to regulate the formation of O-O bond in water oxidation catalysis.

Mass spectrometry studies of nitrene anions

Nitrene anions are a class of reactive intermediates that provide a means for studying the corresponding neutral molecules via electron photodetachment spectroscopy and photoelectron spectroscopy. The added electron makes it possible for protected nitrene anions to be manipulated by external electric and magnetic fields of a mass spectrometer. Nitrene anions also display their own unique reactivities as reagents, which have been investigated using ion/molecule reactions. Mass spectrometry of negative ions has thereby provided information on the electronic states, reactivities, and thermochemical properties of nitrene intermediates. This review also includes a discussion of condensed-phase nitrene anions.

Current Knowledge on Mechanisms Preventing Photosynthesis Redox Imbalance in Plants

Photosynthesis includes a set of redox reactions that are the source of reducing power and energy for the assimilation of inorganic carbon, nitrogen and sulphur, thus generating organic compounds, and oxygen, which supports life on Earth. As sessile organisms, plants have to face continuous changes in environmental conditions and need to adjust the photosynthetic electron transport to prevent the accumulation of damaging oxygen by-products. The balance between photosynthetic cyclic and linear electron flows allows for the maintenance of a proper NADPH/ATP ratio that is adapted to the plant’s needs. In addition, different mechanisms to dissipate excess energy operate in plants to protect and optimise photosynthesis under adverse conditions. Recent reports show an important role of redox-based dithiol–disulphide interchanges, mediated both by classical and atypical chloroplast thioredoxins (TRXs), in the control of these photoprotective mechanisms. Moreover, membrane-anchored TRX-like proteins, such as HCF164, which transfer electrons from stromal TRXs to the thylakoid lumen, play a key role in the regulation of lumenal targets depending on the stromal redox poise. Interestingly, not all photoprotective players were reported to be under the control of TRXs. In this review, we discuss recent findings regarding the mechanisms that allow an appropriate electron flux to avoid the detrimental consequences of photosynthesis redox imbalances.

O2 and Other High-Energy Molecules in Photosynthesis: Why Plants Need Two Photosystems

The energetics of photosynthesis in plants have been re-analyzed in a framework that represents the relatively high energy of O₂ correctly. Starting with the photon energy exciting P680 and "loosening an electron", the energy transfer and electron transport are represented in a comprehensive, self-explanatory sequence of redox energy transfer and release diagrams. The resulting expanded Z-scheme explicitly shows charge separation as well as important high-energy species such as O₂, Tyr_Z˙, and P680⁺˙, whose energies are not apparent in the classical Z-scheme of photosynthesis. Crucially, the energetics of the three important forms of P680 and of P700 are clarified. The relative free energies of oxidized and reduced species are shown explicitly in kJ/mol, not encrypted in volts. Of the chemical energy produced in photosynthesis, more is stored in O₂ than in glucose. The expanded Z-scheme introduced here provides explanatory power lacking in the classical scheme. It shows that P680* is energetically boosted to P680⁺˙ by the favorable electron affinity of pheophytin and that Photosystem I (PSI) has insufficient energy to split H₂O and produce O₂ because P700* is too easily ionized. It also avoids the Z-scheme's bewildering implication, according to the "electron waterfall" concept, that H₂O gives off electrons that spontaneously flow to chlorophyll while releasing energy. The new analysis explains convincingly why plants need two different photosystems in tandem: (i) PSII mostly extracts hydrogen from H₂O, producing PQH₂ (plastoquinol), and generates the energetically expensive product O₂; this step provides little energy directly to the plant; (ii) PSI produces chemical energy for the organism, by pumping protons against a concentration gradient and producing less reluctant hydrogen donors. It also documents that electron transport and energy transfer occur in opposite directions and do not involve redox voltages. The analysis makes it clear that the high-energy species in photosynthesis are unstable, electron-deficient species such as P680⁺˙ and Tyr_Z˙, not putative high-energy electrons.

Evaluation of Manganese Cubanoid Clusters for Water Oxidation Catalysis: From Well-Defined Molecular Coordination Complexes to Catalytically Active Amorphous Films

With a view to developing multimetallic molecular catalysts that mimic the oxygen-evolving catalyst (OEC) in Nature's photosystem II, the synthesis of various dicubanoid manganese clusters is described and their catalytic activity investigated for water oxidation in basic, aqueous solution. Pyridinemethanol-based ligands are known to support polynuclear and cubanoid structures in manganese coordination chemistry. The chelators 2,6-pyridinedimethanol (H₂ L¹ ) and 6-methyl-2-pyridinemethanol (HL² ) were chosen to yield polynuclear manganese complexes; namely, the tetranuclear defective dicubanes [Mn^II ₂ Mn^III ₂ (HL¹ )₄ (OAc)₄ (OMe)₂ ] and [Mn^II ₂ Mn^III ₂ (HL¹ )₆ (OAc)₂ ] (OAc)₂ ⋅2 H₂ O, as well as the octanuclear-dicubanoid [Mn^II ₆ Mn^III ₂ (L² )₄ (O)₂ (OAc)₁₀ (HOMe/OH₂ )₂ ]⋅3MeOH⋅MeCN. In freshly prepared solutions, polynuclear species were detected by electrospray ionization mass spectrometry, whereas X-band electron paramagnetic resonance studies in dilute, liquid solution suggested the presence of divalent mononuclear Mn species with g values of 2. However, the magnetochemical investigation of the complexes' solutions by the Evans technique confirmed a haphazard combination of manganese coordination complexes, from mononuclear to polynuclear species. Subsequently, the newly synthesized and characterized manganese molecular complexes were employed as precursors to prepare electrode-deposited films in a buffer-free solution to evaluate and compare their stability and catalytic activity for water oxidation electrocatalysis.

Generation of Photoelectric Responses by Photosystem II Core Complexes in the Presence of Externally Added Cytochrome c

The effect of exogenous cytochrome c (cyt c) on kinetics of photoelectric responses (Δψ) of two types of photosystem II (PSII) core complexes (intact - PSII with active water-oxidizing complex and Mn-depleted complex) reconstituted into liposomes has been investigated by direct electrometric technique. PSII complexes were localized in the proteoliposome membranes with their donor side outward. An additional electrogenic phase was observed in the kinetics of Δψ generation in response to a laser flash besides the main fast (<0.3 µs) electrogenic component due to electron transfer from the redox-active tyrosine Y_Z to the primary quinone acceptor Q_A in the presence of oxidized cyt c (cyt c³⁺) entrapped in the internal space of proteoliposomes with intact PSII complexes. This component with characteristic time τ ≈ 40 µs and relative amplitude of ~10% of the total Δψ was attributed to the vectorial electron transfer from Q_A^- to cyt c³⁺ serving as an external acceptor. An additional electrogenic component with τ ~ 70 µs and a relative amplitude of ~20% of the total Δψ also appeared in the kinetics of Δψ formation, when cyt c²⁺ was added to the suspension of proteoliposomes containing Mn-depleted PSII core complexes. This component was attributed to the electrogenic transfer of an electron from cyt c²⁺ to photooxidized tyrosine Y_Z. These data imply that cyt c³⁺ serves as a very effective exogenous electron acceptor for Q_A^- in the case of intact PSII core complexes, and cyt c²⁺ is an extremely efficient artificial electron donor for Y_Z in the Mn-depleted PSII. The obtained data on the roles of cyt c²⁺ and cyt c³⁺ as an electron donor and acceptor for PSII, respectively, can be used to develop hybrid photoelectrochemical solar energy-converting systems based on photosynthetic pigment-protein complexes.

Ferromagnetic Coupling in Oxidovanadium(IV)-Porphyrin Radical Dimers

Three different oxidovanadium(IV) porphyrin dimers with anti, cis, and trans arrangements of the two rings have been synthesized by changing the bridge between the porphyrin macrocycles. This provides a unique opportunity to investigate the role of the bridge and spatial arrangement between the two V^IVO centers for their electronic communication and magnetic coupling. They were characterized by the combined application of XRD analysis, UV-vis and electron paramagnetic resonance (EPR) spectroscopy, cyclic voltammetry, magnetic susceptibility, and DFT calculations. One- and two-electron oxidations produce mono- and dication diradical species, respectively, which display an unusual ferromagnetic interaction between the unpaired spins of vanadium(IV) and porphyrin π-cation radical, in contrast to other metalloporphyrin dimers. The oxidized species show a dissimilar behavior between cis and trans isomers. The ferromagnetic coupling occurs between the porphyrin π-cation radical and the unpaired electron of the V^IVO ion on the d_xy orbital, orthogonal to the porphyrin-based molecular orbitals a_1u and a_2u.

The exchange of the fast substrate water in the S2 state of photosystem II is limited by diffusion of bulk water through channels - implications for the water oxidation mechanism

The molecular oxygen we breathe is produced from water-derived oxygen species bound to the Mn4CaO5 cluster in photosystem II (PSII). Present research points to the central oxo-bridge O5 as the 'slow exchanging substrate water (Ws)', while, in the S2 state, the terminal water ligands W2 and W3 are both discussed as the 'fast exchanging substrate water (Wf)'. A critical point for the assignment of Wf is whether or not its exchange with bulk water is limited by barriers in the channels leading to the Mn4CaO5 cluster. In this study, we measured the rates of H2 16O/H2 18O substrate water exchange in the S2 and S3 states of PSII core complexes from wild-type (WT) Synechocystis sp. PCC 6803, and from two mutants, D1-D61A and D1-E189Q, that are expected to alter water access via the Cl1/O4 channels and the O1 channel, respectively. We found that the exchange rates of Wf and Ws were unaffected by the E189Q mutation (O1 channel), but strongly perturbed by the D61A mutation (Cl1/O4 channel). It is concluded that all channels have restrictions limiting the isotopic equilibration of the inner water pool near the Mn4CaO5 cluster, and that D61 participates in one such barrier. In the D61A mutant this barrier is lowered so that Wf exchange occurs more rapidly. This finding removes the main argument against Ca-bound W3 as fast substrate water in the S2 state, namely the indifference of the rate of Wf exchange towards Ca/Sr substitution.

Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

Background

The order Oedogoniales within the single family Oedogoniaceae comprised of three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic studies have suggested that both Oedogonium and Oedocladium may not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes of Oedogonium species and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales.

Results

The five Oedogonium cp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that both Oedocladium and Oedogonium are polyphyletic groups. A positively selected gene (psbA) was identified in the two Oedocladium species and the terrestrial Oedogonium species, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats.

Conclusions

Our results enrich the data on cp genomes of the genus Oedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08006-1.

Modeling magnetic interactions in high-valent trinuclear [Mn3(IV)O4]4+ complexes through highly compressed multi-configurational wave functions

In this work we apply a quantum chemical framework, recently designed in our laboratories, to rationalize the low-energy electronic spectrum and the magnetic properties of an homo-valent trinuclear [Mn₃^(IV)O₄]⁴⁺ model of the oxygen-evolving center in photosystem II. The method is based on chemically motivated molecular orbital unitary transformations, and the optimization of spin-adapted many-body wave functions, both for ground- and excited-states, in the transformed MO basis. In this basis, the configuration interaction Hamiltonian matrix of exchange-coupled multi-center clusters is extremely sparse and characterized by a unique block diagonal structure. This property leads to highly compressed wave functions (oligo- or single-reference) and crucially enables state-specific optimizations. This work is the first showing that compression and selective targeting of ground- and excited-states wave functions is possible for systems with three magnetic centers that are not exactly half-filled, and that potentially exhibit frustrated spin interactions. The reduced multi-reference character of the wave function greatly simplifies the interpretation of the ground- and excited-state electronic structures, and provides a route for the direct rationalization of magnetic interactions in these compounds, often considered a challenge in polynuclear transition-metal chemistry. In this study, strong electron correlation effects have explicitly been described by conventional and stochastic multiconfigurational methodologies, while dynamic correlation effects have been accounted for by multiconfigurational second order perturbation theory, CASPT2. Ab initio results for the [Mn₃^(IV)O₄]⁴⁺ system have been mapped to a three-site Heisenberg model with two magnetic coupling constants. The magnetic coupling constants and the temperature dependence of the effective magnetic moment predicted by the ab initio calculations are in good agreement with the available experimental data, and confirm the antiferromagnetic interaction among the three magnetic centers, while providing a simple and rigorous description of the noncollinearity of the local spins, that characterize most of the low-energy states for this system.

Identifying Intermediates in Electrocatalytic Water Oxidation with a Manganese Corrole Complex

Water nucleophilic attack (WNA) on high-valent terminal Mn-oxo species is proposed for O-O bond formation in natural and artificial water oxidation. Herein, we report an electrocatalytic water oxidation reaction with Mn^III tris(pentafluorophenyl)corrole (1) in propylene carbonate (PC). O₂ was generated at the Mn^V/IV potential with hydroxide, but a more anodic potential was required to evolve O₂ with only water. With a synthetic Mn^V(O) complex of 1, a second-order rate constant, k₂(OH^-), of 7.4 × 10³ M^-1 s^-1 was determined in the reaction of the Mn^V(O) complex of 1 with hydroxide, whereas its reaction with water occurred much more slowly with a k₂(H₂O) value of 4.4 × 10^-3 M^-1 s^-1. This large reactivity difference of Mn^V(O) with hydroxide and water is consistent with different electrocatalytic behaviors of 1 with these two substrates. Significantly, during the electrolysis of 1 with water, a Mn^IV-peroxo species was identified with various spectroscopic methods, including UV-vis, electron paramagnetic resonance, and infrared spectroscopy. Isotope-labeling experiments confirmed that both O atoms of this peroxo species are derived from water, suggesting the involvement of the WNA mechanism in water oxidation by a Mn complex. Density functional theory calculations suggested that the nucleophilic attack of hydroxide on Mn^V(O) and also WNA to 1e^--oxidized Mn^V(O) are feasibly involved in the catalytic cycles but that direct WNA to Mn^V(O) is not likely to be the main O-O bond formation pathway in the electrocatalytic water oxidation by 1.

Controlled Regulation of the Nitrile Activation of a Peroxocobalt(III) Complex with Redox-Inactive Lewis Acidic Metals

Redox-inactive metal ions play vital roles in biological O₂ activation and oxidation reactions of various substrates. Recently, we showed a distinct reactivity of a peroxocobalt(III) complex bearing a tetradentate macrocyclic ligand, [Co^III(TBDAP)(O₂)]⁺ (1) (TBDAP = N,N'-di-tert-butyl-2,11-diaza[3.3](2,6)pyridinophane), toward nitriles that afforded a series of hydroximatocobalt(III) complexes, [Co^III(TBDAP)(R-C(═NO)O)]⁺ (R = Me (3), Et, and Ph). In this study, we report the effects of redox-inactive metal ions on nitrile activation of 1. In the presence of redox-inactive metal ions such as Zn²⁺, La³⁺, Lu³⁺, and Y³⁺, the reaction does not form the hydroximatocobalt(III) complex but instead gives peroxyimidatocobalt(III) complexes, [Co^III(TBDAP)(R-C(═NH)O₂)]²⁺ (R = Me (2) and Ph (2^Ph)). These new intermediates were characterized by various physicochemical methods including X-ray diffraction analysis. The rates of the formation of 2 are found to correlate with the Lewis acidity of the additive metal ions. Moreover, complex 2 was readily converted to 3 by the addition of a base. In the presence of Al³⁺, Sc³⁺, or H⁺, 1 is converted to [Co^III(TBDAP)(O₂H)(MeCN)]²⁺ (4), and further reaction with nitriles did not occur. These results reveal that the reactivity of the peroxocobalt(III) complex 1 in nitrile activation can be regulated by the redox-inactive metal ions and their Lewis acidity. DFT calculations show that the redox-inactive metal ions stabilize the peroxo character of end-on Co-η¹-O₂ intermediate through the charge reorganization from a Co^II-superoxo to a Co^III-peroxo intermediate. A complete mechanistic model explaining the role of the Lewis acid is presented.

Photosystem II-based biomimetic assembly for enhanced photosynthesis

Photosystem II (PSII) is a fascinating photosynthesis-involved enzyme, participating in sunlight-harvest, water splitting, oxygen release, and proton/electron generation and transfer. Scientists have been inspired to couple PSII with synthetic hierarchical structures via biomimetic assembly, facilitating attainment of natural photosynthesis processes, such as photocatalytic water splitting, electron transfer and ATP synthesis, in vivo. In the past decade, there has been significant progress in PSII-based biomimetic systems, such as artificial chloroplasts and photoelectrochemical cells. The biomimetic assembly approach helps PSII gather functions and properties from synthetic materials, resulting in a complex with partly natural and partly synthetic components. PSII-based biomimetic assembly offers opportunities to forward semi-biohybrid research and synchronously inspire optimization of artificial light-harvest micro/nanodevices. This review summarizes recent studies on how PSII combines with artificial structures via molecular assembly and highlights PSII-based semi-natural biosystems which arise from synthetic parts and natural components. Moreover, we discuss the challenges and remaining problems for PSII-based systems and the outlook for their development and applications. We believe this topic provides inspiration for rational designs to develop biomimetic PSII-based semi-natural devices and further reveal the secrets of energy conversion within natural photosynthesis from the molecular level.

The hydrophobicity of mutations targeting D1:Val219 modifies formate and diuron binding in the quinone-Fe-acceptor complex of Photosystem II

The D1:Val219 residue of Photosystem II in the cyanobacterium Synechocystis sp. PCC 6803 was mutated to alanine or isoleucine, creating the V219A and V219I mutants, respectively. Oxygen evolution was slowed in these mutants, while chlorophyll a fluorescence induction assays indicated slowed electron transfer. As previously observed [Erickson J.M., Rahire, M., Rochaix, J.-D. and Mets. L. (1985) Science, 228, 204-207], the V219I mutant was resistant to 3,4-dichloro-1,1-dimethyl urea (DCMU); however, the V219A strain displayed no DCMU resistance. Additionally, the V219A strain was less sensitive to the addition of formate than the control, while the V219I strain was more sensitive to formate. Both mutant strains were susceptible to photodamage and required protein synthesis for recovery. We hypothesize that the sensitivity to DCMU and the extent of bicarbonate-reversible formate-induced inhibition, as well as the capacity for recovery in cells following photodamage, are influenced by the hydrophobicity of the environment associated with the Val219 residue in D1.

Mechanism of Oxygen Evolution and Mn4CaO5 Cluster Restoration in the Natural Water-Oxidizing Catalyst

Water oxidation occurring in the first steps of natural oxygenic photosynthesis is catalyzed by the pigment/protein complex Photosystem II. This process takes place on the Mn₄Ca cluster located in the core of Photosystem II and proceeds along the five steps (S₀-S₄) of the so-called Kok-Joliot cycle until the release of molecular oxygen. The catalytic cycle can therefore be started afresh through insertion of a new water molecule. Here, combining quantum mechanics/molecular mechanics simulations and minimum energy path calculations, we characterized on different spin surfaces the events occurring in the last sector of the catalytic cycle from structural, electronic, and thermodynamic points of view. We found that the process of oxygen evolution and water insertion can be described well by a two-step mechanism, with oxygen release being the rate-limiting step of the process. Moreover, our results allow us to identify the upcoming water molecule required to regenerate the initial structure of the Mn₄Ca cluster in the S₀ state. The insertion of the water molecule was found to be coupled with the transfer of a proton to a neighboring hydroxide ion, thus resulting in the reconstitution of the most widely accepted model of the S₀ state.

Biohybrid Systems for Improved Bioinspired, Energy-Relevant Catalysis

Biomimetic catalysts, ranging from small-molecule metal complexes to supramolecular assembles, possess many exciting properties that could address salient challenges in industrial-scale manufacturing. Inspired by natural enzymes, these biohybrid catalytic systems demonstrate superior characteristics, including high activity, enantioselectivity, and enhanced aqueous solubility, over their fully synthetic counterparts. However, instability and limitations in the prediction of structure-function relationships are major drawbacks that often prevent the application of biomimetic catalysts outside of the laboratory. Despite these obstacles, recent advances in synthetic enzyme models have improved our understanding of complicated biological enzymatic processes and enabled the production of catalysts with increased efficiency. This review outlines important developments and future prospects for the design and application of bioinspired and biohybrid systems at multiple length scales for important, biologically relevant, clean energy transformations.

Highly Efficient S-g-CN/Mo-368 Catalyst for Synergistically NADH Regeneration Under Solar Light

Sulfur-doped graphitic carbon nitride (S-g-CN) has gained significant attention in recent years. Sulfur-doped graphitic carbon nitride (S-g-CN) is a promising metal-free photocatalyst because of its band orientation, natural abundance and groundwork. Improved photocatalytic activity of S-g-CN material for solar chemical production persists a hot yet challenging problem. Herein, we provide an adaptable method for the synthesis of S-g-CN nanocomposite decorated with the moiety of giant polyoxometalate (S-g-CN/Mo-368) that subsequently showed highly efficient photocatalytic activity. The as-synthesized S-g-CN/Mo-368 as a recyclable artificial photocatalyst revealed excellent activity for solar chemical production, that is nicotinamide adenine dinucleotide (NADH) regeneration under visible light. The immobilized Mo-368 on the S-g-CN surface increased the visible light adsorption capacity of the S-g-CN/Mo-368 photocatalyst. The visible light absorption activity, morphology, element compositions, particle size and zeta potential of S-g-CN powder and S-g-CN/Mo-368 were thoroughly investigated. From the application point of view, S-g-CN/Mo-368 was applied to determine the solar chemical production (i.e. NADH regeneration) under visible light with a higher yield% of about ~ 94.85%.

Characterizing the supercomplex association of photosynthetic complexes in cyanobacteria

The light reactions of photosynthesis occur in thylakoid membranes that are densely packed with a series of photosynthetic complexes. The lateral organization and close association of photosynthetic complexes in native thylakoid membranes are vital for efficient light harvesting and energy transduction. Recently, analysis of the interconnections between photosynthetic complexes to form supercomplexes has garnered great interest. In this work, we report a method integrating immunoprecipitation, mass spectrometry and atomic force microscopy to identify the inter-complex associations of photosynthetic complexes in thylakoid membranes from the cyanobacterium Synechococcus elongatus PCC 7942. We characterize the preferable associations between individual photosynthetic complexes and binding proteins involved in the complex-complex interfaces, permitting us to propose the structural models of photosynthetic complex associations that promote the formation of photosynthetic supercomplexes. We also identified other potential binding proteins with the photosynthetic complexes, suggesting the highly connecting networks associated with thylakoid membranes. This study provides mechanistic insight into the physical interconnections of photosynthetic complexes and potential partners, which are crucial for efficient energy transfer and physiological acclimatization of the photosynthetic apparatus. Advanced knowledge of the protein organization and interplay of the photosynthetic machinery will inform rational design and engineering of artificial photosynthetic systems to supercharge energy production.

Time-resolved comparative molecular evolution of oxygenic photosynthesis

Oxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are the only prokaryotes capable of water oxidation and therefore, it is assumed that the origin of oxygenic photosynthesis is a late innovation relative to the origin of life and bioenergetics. However, when exactly water oxidation originated remains an unanswered question. Here we use phylogenetic analysis to study a gene duplication event that is unique to photosystem II: the duplication that led to the evolution of the core antenna subunits CP43 and CP47. We compare the changes in the rates of evolution of this duplication with those of some of the oldest well-described events in the history of life: namely, the duplication leading to the Alpha and Beta subunits of the catalytic head of ATP synthase, and the divergence of archaeal and bacterial RNA polymerases and ribosomes. We also compare it with more recent events such as the duplication of Cyanobacteria-specific FtsH metalloprotease subunits and the radiation leading to Margulisbacteria, Sericytochromatia, Vampirovibrionia, and other clades containing anoxygenic phototrophs. We demonstrate that the ancestral core duplication of photosystem II exhibits patterns in the rates of protein evolution through geological time that are nearly identical to those of the ATP synthase, RNA polymerase, or the ribosome. Furthermore, we use ancestral sequence reconstruction in combination with comparative structural biology of photosystem subunits, to provide additional evidence supporting the premise that water oxidation had originated before the ancestral core duplications. Our work suggests that photosynthetic water oxidation originated closer to the origin of life and bioenergetics than can be documented based on phylogenetic or phylogenomic species trees alone.

Photoelectrochemical Water Oxidation by Cobalt Cytochrome C Integrated-ATO Photoanode

Here, we report the immobilization of Co-protoporphyrin IX (Co-PPIX) substituted cytochrome c (Co-cyt c) on Antimony-doped Tin Oxide (ATO) as a catalyst for photoelectrochemical oxidation of water. Under visible light irradiation (λ > 450 nm), the ATO-Co-cyt c photoanode displays ~6-fold enhancement in photocurrent density relative to ATO-Co-PPIX at 0.25 V vs. RHE at pH 5.0. The light-induced water oxidation activity of the system was demonstrated by detecting evolved stoichiometric oxygen by gas chromatography, and incident photon to current efficiency was measured as 4.1% at 450 nm. The faradaic efficiency for the generated oxygen was 97%, with a 671 turnover number (TON) for oxygen. The current density had a slow decay over the course of 6 h of constant irradiation and applied potential, which exhibits the robustness of catalyst-ATO interaction.

Metabolome and transcriptome profiling reveals anthocyanin contents and anthocyanin-related genes of chimeric leaves in Ananas comosus var. bracteatus

BACKGROUND

Ananas comosus var. bracteatus is a colorful plant used as a cut flower or landscape ornamental. The unique foliage color of this plant includes both green and red leaves and, as a trait of interest, deserves investigation. In order to explore the pigments behind the red section of the chimeric leaves, the green and red parts of chimeric leaves of Ananas comosus var. bracteatus were sampled and analyzed at phenotypic, cellular and molecular levels in this study.

RESULTS

The CIELAB results indicated that the a* values and L* values samples had significant differences between two parts. Freehand sections showed that anthocyanin presented limited accumulation in the green leaf tissues but obviously accumulation in the epidermal cells of red tissues. Transcriptomic and metabolomic analyses were performed by RNA-seq and LC-ESI-MS/MS. Among the 508 identified metabolites, 10 kinds of anthocyanins were detected, with 6 significantly different between the two samples. The cyanidin-3,5-O-diglucoside content that accounts for nearly 95.6% in red samples was significantly higher than green samples. RNA-Seq analyses showed that 11 out of 40 anthocyanin-related genes were differentially expressed between the green and red samples. Transcriptome and metabolome correlations were determined by nine quadrant analyses, and 9 anthocyanin-related genes, including MYB5 and MYB82, were correlated with 7 anthocyanin-related metabolites in the third quadrant in which genes and metabolites showing consistent change. Particularly, the PCCs between these two MYB genes and cyanidin-3,5-O-diglucoside were above 0.95.

CONCLUSION

Phenotypic colors are closely related to the tissue structures of different leaf parts of Ananas comosus var. bracteatus, and two MYB transcription factors might contribute to differences of anthocyanin accumulation in two parts of Ananas comosus var. bracteatus chimeric leaves. This study lay a foundation for further researches on functions of MYBs in Ananas comosus var. bracteatus and provides new insights to anthocyanin accumulation in different parts of chimeric leaves.

Orientational Jahn-Teller Isomerism in the Dark-Stable State of Nature's Water Oxidase

The tetramanganese–calcium cluster of the oxygen‐evolving complex of photosystem II adopts electronically and magnetically distinct but interconvertible valence isomeric forms in its first light‐driven oxidized catalytic state, S₂. This bistability is implicated in gating the final catalytic states preceding O−O bond formation, but it is unknown how the biological system enables its emergence and controls its effect. Here we show that the Mn₄CaO₅ cluster in the resting (dark‐stable) S₁ state adopts orientational Jahn–Teller isomeric forms arising from a directional change in electronic configuration of the “dangler” Mn^III ion. The isomers are consistent with available structural data and explain previously unresolved electron paramagnetic resonance spectroscopic observations on the S₁ state. This unique isomerism in the resting state is shown to be the electronic origin of valence isomerism in the S₂ state, establishing a functional role of orientational Jahn–Teller isomerism unprecedented in biological or artificial catalysis.

A Computational Study of the S2 State in the Oxygen-Evolving Complex of Photosystem II by Electron Paramagnetic Resonance Spectroscopy

The S2 state produces two basic electron paramagnetic resonance signal types due to the manganese cluster in oxygen-evolving complex, which are influenced by the solvents, and cryoprotectant added to the photosystem II samples. It is presumed that a single manganese center oxidation occurs on S1 → S2 state transition. The S2 state has readily visible multiline and g4.1 electron paramagnetic resonance signals and hence it has been the most studied of all the Kok cycle intermediates due to the ease of experimental preparation and stability. The S2 state was studied using electron paramagnetic resonance spectroscopy at X-band frequencies. The aim of this study was to determine the spin states of the g4.1 signal. The multiline signal was observed to arise from a ground state spin ½ centre while the g4.1 signal generated at ≈140 K NIR illumination was proposed to arise from a spin 52 center with rhombic distortion. The 'ground' state g4.1 signal was generated solely or by conversion from the multiline. The data analysis methods used involved numerical simulations of the experimental spectra on relevant models of the oxygen-evolving complex cluster. A strong focus in this paper was on the 'ground' state g4.1 signal, whether it is a rhombic 52 spin state signal or an axial 32 spin state signal. The data supported an X-band CW-EPR-generated g4.1 signal as originating from a near rhombic spin 5/2 of the S2 state of the PSII manganese cluster.

Diverged Early From CtpB and CtpC, CtpA Has Evolved to Process D1 Precursor in Oxygenic Photosynthetic Organisms

C-terminal peptidase (Ctp) cleaves the C-terminal extension of the D1 precursor (pD1) to form mature D1. Among the three homologs CtpA, CtpB, and CtpC in photosynthetic organisms only the first is capable of processing pD1 while the roles of CtpB and CtpC remain elusive. Phylogenetic analysis of Ctps from photosynthetic organisms revealed that CtpA has diverged early from CtpB and CtpC during evolution implying distinct roles for the Ctps. Analysis of Arabidopsis Ctp-deficient mutants revealed that pD1 processing was not affected in atctpb, atctpc, or atctpbatctpc mutants, demonstrating that AtCtpA, not AtCtpB or AtCtpC, is responsible for cleaving the pD1 C-terminal extension. Ectopic expression of CtpAs from Synechococcus elongatus, Chlamydomonas reinhardtii, and Physcomitrella patens in atctpa rescued the lethal phenotype of the mutant indicating that SeCtpA, CrCtpA, and PpCtpA could process pD1 in Arabidopsis. Enzyme activity assays showed that PpCtpA and CrCtpA could convert pD1 into mature D1 in vitro. In contrast, expressing CtpB or CtpC from Arabidopsis, C. reinhardtii, or P. patens in atctpa did not rescue its D1 maturation deficiency, and enzyme activity assays also showed that neither CtpB nor CtpC could process pD1 in vitro. Taken together, we conclude that the function of pD1 processing by CtpA is conserved in photosynthetic organisms. It is possible that among other factors CtpA developed this function to initiate the formation of the oxygenic D1/D2 type PSII complex during evolution whereas CtpB or CtpC have other roles that are still unclear.

Structural insights into photosystem II assembly

Biogenesis of photosystem II (PSII), nature's water-splitting catalyst, is assisted by auxiliary proteins that form transient complexes with PSII components to facilitate stepwise assembly events. Using cryo-electron microscopy, we solved the structure of such a PSII assembly intermediate from Thermosynechococcus elongatus at 2.94 Å resolution. It contains three assembly factors (Psb27, Psb28 and Psb34) and provides detailed insights into their molecular function. Binding of Psb28 induces large conformational changes at the PSII acceptor side, which distort the binding pocket of the mobile quinone (Q_B) and replace the bicarbonate ligand of non-haem iron with glutamate, a structural motif found in reaction centres of non-oxygenic photosynthetic bacteria. These results reveal mechanisms that protect PSII from damage during biogenesis until water splitting is activated. Our structure further demonstrates how the PSII active site is prepared for the incorporation of the Mn₄CaO₅ cluster, which performs the unique water-splitting reaction.