256 results found
Sjödin M, Hjelm J, Rutherford AW, et al., 2020, Proton-coupled electron transfer from an interfacial phenol monolayer, Journal of Electroanalytical Chemistry, Vol: 859, ISSN: 1572-6657
© 2020 Elsevier B.V. A tert-butyl protected phenol is covalently link to a mixed self-assembled monolayer on a gold or platinum electrode. The phenol reduction potential shows the expected pH-dependence of a one-electron, one-proton couple with a decrease in formal reduction potential of 59 ± 5 mV per pH. A titration of the phenol is observed with a pKa of 13.2 and the reduction potential for the phenolate is 0.11 V. NHE. The kinetic behavior of the proton-coupled oxidation deviates substantially from the commonly used models for a step-wise reaction that assume the proton transfer reactions are in equilibrium throughout the reaction. A novel model for step-wise proton-coupled reactions is presented that fully accounts for the pH dependent kinetics and allows the formal rate constants and the transfer coefficients to be determined.
Cardona Londono T, Rutherford AW, 2019, Evolution of photochemical reaction centres: more twists?, Trends in Plant Science, Vol: 24, Pages: 1008-1021, ISSN: 1878-4372
One of the earliest events in the molecular evolution of photosynthesis is the structural and functional specialisation of Type I (ferredoxin-reducing) and Type II (quinone-reducing) reaction centres. In this opinion article we point out that the homodimeric Type I reaction centre of Heliobacteria has a calcium-binding site with striking structural similarities to the Mn4CaO5 cluster of Photosystem II. These similarities indicate that most of the structural elements required to evolve water oxidation chemistry were present in the earliest reaction centres. We suggest that the divergence of Type I and Type II reaction centres was made possible by a drastic structural shift linked to a change in redox properties that coincided with or facilitated the origin of photosynthetic water oxidation.
De Causmaecker S, Douglass J, Fantuzzi A, et al., 2019, Energetics of the exchangeable quinone, QB, in Photosystem II, Proceedings of the National Academy of Sciences of USA, Vol: 116, Pages: 19458-19463, ISSN: 0027-8424
Photosystem II (PSII), the light-driven water/plastoquinone photo-oxidoreductase, is of central importance in the planetary energy cycle. The product of the reaction, plastohydroquinone (PQH2), is released into the membrane from the QB-site, where it is formed. A plastoquinone (PQ) from the membrane pool then binds into the QB-site. Despite their functional importance, the thermodynamic properties of the PQ in the QB-site, QB, in its different redox forms have received relatively little attention. Here we report the midpoint potentials (Em) of QB in PSII from Thermosynechococcus elongatus using EPR spectroscopy: Em QB/QB•−≈ 90 mV and Em QB•−/QBH2≈ 40 mV. These data allow the following conclusions: 1) the semiquinone, QB•−, is stabilized thermodynamically; 2) the resulting Em QB/QBH2 (~ 65 mV) is lower than the EmPQ/PQH2 (~117 mV), and the difference (ΔE ~50 meV) represents the driving force for QBH2 release into the pool; 3) PQ is ~ 50x more tightly bound than PQH2; 4) the difference between the Em QB/QB•− measured here and the Em QA/QA•− from the literature is ~234 meV, in principle corresponding to the driving force for electron transfer from QA•− to QB. The pH-dependence of the thermoluminescence associated with QB•− provided a functional estimate for this energy gap and gave a similar value (≥180 meV). These estimates are larger than the generally accepted value (~70 meV) and this is discussed. The energetics of QB in PSII are comparable to those in the homologous purple bacterial reaction center.
Varghese F, Kabasakal BV, Cotton CA, et al., 2019, A low-potential terminal oxidase associated with the iron-only nitrogenase from the nitrogen-fixing bacterium Azotobacter vinelandii, Journal of Biological Chemistry, ISSN: 0021-9258
The biological route for nitrogen gas entering the biosphere is reduction to ammonia by the nitrogenase enzyme, which is inactivated by oxygen. Three types of nitrogenase exist, the least studied of which is the iron-only nitrogenase. The Anf3 protein in the bacterium Rhodobacter capsulatus is essential for diazotrophic (i.e. nitrogen-fixing) growth with the iron-only nitrogenase, but its enzymatic activity and function are unknown. Here, we biochemically and structurally characterize Anf3 from the model diazotrophic bacterium Azotobacter vinelandii. Determining the Anf3 crystal structure to atomic resolution, we observed that it is a dimeric flavocytochrome with an unusually close interaction between the heme and the flavin adenine dinucleotide cofactors. Measuring the reduction potentials by spectroelectrochemical redox titration, we observed values of -420 ± 10 mV and -330 ± 10 mV for the two FAD potentials and -340 ± 1 mV for the heme. We further show that Anf3 accepts electrons from spinach ferredoxin and that Anf3 consumes oxygen without generating superoxide or hydrogen peroxide. We predict that Anf3 protects the iron-only nitrogenase from oxygen inactivation by functioning as an oxidase in respiratory protection, with flavodoxin or ferredoxin as the physiological electron donors.
Takegawa Y, Nakamura M, Nakamura S, et al., 2019, New insights on ChlD1 function in Photosystem II from site-directed mutants of D1/T179 in Thermosynechococcus elongatus, Biochimica et Biophysica Acta - Bioenergetics, Vol: 1860, Pages: 297-309, ISSN: 0005-2728
The monomeric chlorophyll, ChlD1, which is located between the PD1PD2 chlorophyll pair and the pheophytin, PheoD1, is the longest wavelength chlorophyll in the heart of Photosystem II and is thought to be the primary electron donor. Its central Mg2+ is liganded to a water molecule that is H-bonded to D1/T179. Here, two site-directed mutants, D1/T179H and D1/T179V, were made in the thermophilic cyanobacterium, Thermosynechococcus elongatus, and characterized by a range of biophysical techniques. The Mn4CaO5 cluster in the water-splitting site is fully active in both mutants. Changes in thermoluminescence indicate that i) radiative recombination occurs via the repopulation of *ChlD1 itself; ii) non-radiative charge recombination reactions appeared to be faster in the T179H-PSII; and iii) the properties of PD1PD2 were unaffected by this mutation, and consequently iv) the immediate precursor state of the radiative excited state is the ChlD1+PheoD1- radical pair. Chlorophyll bleaching due to high intensity illumination correlated with the amount of 1O2 generated. Comparison of the bleaching spectra with the electrochromic shifts attributed to ChlD1 upon QA- formation, indicates that in the T179H-PSII and in the WT*3-PSII, the ChlD1 itself is the chlorophyll that is first damaged by 1O2, whereas in the T179V-PSII a more red chlorophyll is damaged, the identity of which is discussed. Thus, ChlD1 appears to be one of the primary damage site in recombination-mediated photoinhibition. Finally, changes in the absorption of ChlD1 very likely contribute to the well-known electrochromic shifts observed at ~430 nm during the S-state cycle.
Photosystem II is a photochemical reaction center that catalyzes the light‐driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale, we hypothesize that this early Archean photosystem was capable of water oxidation to oxygen and had already evolved protection mechanisms against the formation of reactive oxygen species. This would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.
Zamzam N, Kaucikas M, Nurnberg D, et al., 2019, Femtosecond infrared spectroscopy of chlorophyll f-containing photosystem I, Physical Chemistry Chemical Physics, Vol: 21, Pages: 1224-1234, ISSN: 1463-9076
The recent discovery of extremely red-shifted chlorophyll f pigments in both photosystem I (PSI) and photosystem II has led to the conclusion that chlorophyll f plays a role not only in the energy transfer, but also in the charge separation processes [Nürnberg et al., Science, 2018, 360, 1210–1213]. We have employed ultrafast transient infrared absorption spectroscopy to study the contribution of far-red light absorbing chlorophyll f to energy transfer and charge separation processes in far-red light-grown PSI (FRL-PSI) from the cyanobacterium Chroococcidiopsis thermalis PCC 7203. We compare the kinetics and spectra of FRL-grown PSI excited at 670 nm and 740 nm wavelengths to those of white light-grown PSI (WL-PSI) obtained at 675 nm excitation. We report a fast decay of excited state features of chlorophyll a and complete energy transfer from chlorophyll a to chlorophyll f in FRL-PSI upon 670 nm excitation, as indicated by a frequency shift in a carbonyl absorption band occurring within a 1 ps timescale. While the WL-PSI measurements support the assignment of initial charge separation to A−1+˙A0−˙ [Di Donato et al., Biochemistry, 2011, 50, 480–490] from the kinetics of a distinct cation feature at 1710 cm−1, in the case of FRL-PSI, small features at 1715 cm−1 from the chlorophyll cation are present from sub-ps delays instead, supporting the replacement of the A−1 pigment with chlorophyll f. Comparisons of nanosecond spectra show that charge separation proceeds with 740 nm excitation, which selectively excites chlorophyll f, and modifications in specific carbonyl absorption bands assigned to P700+˙ minus P700 and A1−˙ minus A1 indicate dielectric differences of FRL-PSI compared to WL-PSI in one or both of the two electron transfer branches of FRL-PSI.
Kornienko N, Zhang JZ, Sokol K, et al., 2018, Oxygenic photoreactivity in photosystem II studied by rotating ring disk electrochemistry, Journal of the American Chemical Society, Vol: 140, Pages: 17923-17931, ISSN: 1520-5126
Protein film photoelectrochemistry has previously been used to monitor the activity of Photosystem II, the water-plastoquinone photooxidoreductase, but the mechanistic information attainable from a three-electrode setup has remained limited. Here we introduce the four-electrode rotating ring disk electrode technique for quantifying light-driven reaction kinetics and mechanistic pathways in real time at the enzyme-electrode interface. This setup allows us to study photochemical H2O oxidation in Photosystem II and to gain in-depth understanding of pathways that generate reactive oxygen species. The results show that Photosystem II reacts with O2 through two main pathways that both involve a superoxide intermediate to produce H2O2. The first pathway involves the established chlorophyll triplet-mediated formation of singlet oxygen, which is followed by its reduction to superoxide at the electrode surface. The second pathway is specific for the enzyme/electrode interface: an exposed antenna chlorophyll is sufficiently close to the electrode for rapid injection of an electron to form a highly reducing chlorophyll anion, which reacts with O2 in solution to produce O2•-. Incomplete H2O oxidation does not significantly contribute to reactive oxygen formation in our conditions. The rotating ring disk electrode technique allows the chemical reactivity of Photosystem II to be studied electrochemically and opens several avenues for future investigation.
Cardona T, Rutherford AW, 2018, Evolution of photochemical reaction centres: more twists?, Publisher: Cold Spring Harbor Laboratory
<jats:p>The earliest event recorded in the molecular evolution of photosynthesis is the structural and functional specialisation of Type I (ferredoxin-reducing) and Type II (quinone-reducing) reaction centres. Here we point out that the homodimeric Type I reaction centre of Heliobacteria has a Ca2+-binding site with a number of striking parallels to the Mn4CaO5 cluster of cyanobacterial Photosystem II. This structural parallels indicate that water oxidation chemistry originated at the divergence of Type I and Type II reaction centres. We suggests that this divergence was triggered by a structural rearrangement of a core transmembrane helix resulting in a shift of the redox potential of the electron donor side and electron acceptor side at the same time and in the same redox direction.</jats:p>
Messant M, Timm S, Fantuzzi A, et al., 2018, Glycolate Induces Redox Tuning Of Photosystem II in Vivo: Study of a Photorespiration Mutant, PLANT PHYSIOLOGY, Vol: 177, Pages: 1277-1285, ISSN: 0032-0889
Nuernberg DJ, Morton J, Santabarbara S, et al., 2018, Photochemistry beyond the red limit in chlorophyll f-containing photosystems, Science, Vol: 360, Pages: 1210-1213, ISSN: 0036-8075
Photosystems I and II convert solar energy into the chemical energy that powers life. Chlorophyll a photochemistry, using red light (680 to 700 nm), is near universal and is considered to define the energy “red limit” of oxygenic photosynthesis. We present biophysical studies on the photosystems from a cyanobacterium grown in far-red light (750 nm). The few long-wavelength chlorophylls present are well resolved from each other and from the majority pigment, chlorophyll a. Charge separation in photosystem I and II uses chlorophyll f at 745 nm and chlorophyll f (or d) at 727 nm, respectively. Each photosystem has a few even longer-wavelength chlorophylls f that collect light and pass excitation energy uphill to the photochemically active pigments. These photosystems function beyond the red limit using far-red pigments in only a few key positions.
Boussac A, Ugur I, Marion A, et al., 2018, The low spin - high spin equilibrium in the S2-state of the water oxidizing enzyme, Biochim Biophys Acta, Vol: 1859, Pages: 342-356, ISSN: 0006-3002
In Photosystem II (PSII), the Mn4CaO5-cluster of the active site advances through five sequential oxidation states (S0to S4) before water is oxidized and O2is generated. Here, we have studied the transition between the low spin (LS) and high spin (HS) configurations of S2using EPR spectroscopy, quantum chemical calculations using Density Functional Theory (DFT), and time-resolved UV-visible absorption spectroscopy. The EPR experiments show that the equilibrium between S2LSand S2HSis pH dependent, with a pKa ≈ 8.3 (n ≈ 4) for the native Mn4CaO5and pKa ≈ 7.5 (n ≈ 1) for Mn4SrO5. The DFT results suggest that exchanging Ca with Sr modifies the electronic structure of several titratable groups within the active site, including groups that are not direct ligands to Ca/Sr, e.g., W1/W2, Asp61, His332 and His337. This is consistent with the complex modification of the pKaupon the Ca/Sr exchange. EPR also showed that NH3addition reversed the effect of high pH, NH3-S2LSbeing present at all pH values studied. Absorption spectroscopy indicates that NH3is no longer bound in the S3TyrZstate, consistent with EPR data showing minor or no NH3-induced modification of S3and S0. In both Ca-PSII and Sr-PSII, S2HSwas capable of advancing to S3at low temperature (198 K). This is an experimental demonstration that the S2LSis formed first and advances to S3via the S2HSstate without detectable intermediates. We discuss the nature of the changes occurring in the S2LSto S2HStransition which allow the S2HSto S3transition to occur below 200 K. This work also provides a protocol for generating S3in concentrated samples without the need for saturating flashes.
Zhang JZ, Bombelli P, Sokol KP, et al., 2018, Photoelectrochemistry of Photosystem II &ITin Vitro&IT vs&IT in Vivo&IT, Journal of the American Chemical Society, Vol: 140, Pages: 6-9, ISSN: 1520-5126
Factors governing the photoelectrochemical output of photosynthetic microorganisms are poorly understood, and energy loss may occur due to inefficient electron transfer (ET) processes. Here, we systematically compare the photoelectrochemistry of photosystem II (PSII) protein-films to cyanobacteria biofilms to derive: (i) the losses in light-to-charge conversion efficiencies, (ii) gains in photocatalytic longevity, and (iii) insights into the ET mechanism at the biofilm interface. This study was enabled by the use of hierarchically structured electrodes, which could be tailored for high/stable loadings of PSII core complexes and Synechocystis sp. PCC 6803 cells. The mediated photocurrent densities generated by the biofilm were 2 orders of magnitude lower than those of the protein-film. This was partly attributed to a lower photocatalyst loading as the rate of mediated electron extraction from PSII in vitro is only double that of PSII in vivo. On the other hand, the biofilm exhibited much greater longevity (>5 days) than the protein-film (<6 h), with turnover numbers surpassing those of the protein-film after 2 days. The mechanism of biofilm electrogenesis is suggested to involve an intracellular redox mediator, which is released during light irradiation.
Lohmiller T, Krewald V, Sedoud A, et al., 2017, The First State in the Catalytic Cycle of the Water-Oxidizing Enzyme: Identification of a Water-Derived mu-Hydroxo Bridge, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 139, Pages: 14412-14424, ISSN: 0002-7863
Davis GA, Rutherford AW, Kramer DM, 2017, Hacking the thylakoid proton motive force for improved photosynthesis: modulating ion flux rates that control proton motive force partitioning into Delta psi and Delta pH, Philosophical Transactions of the Royal Society of London: Biological Sciences, Vol: 372, ISSN: 0962-8436
There is considerable interest in improving plant productivity by altering the dynamic responses of photosynthesis in tune with natural conditions. This is exemplified by the ‘energy-dependent' form of non-photochemical quenching (qE), the formation and decay of which can be considerably slower than natural light fluctuations, limiting photochemical yield. In addition, we recently reported that rapidly fluctuating light can produce field recombination-induced photodamage (FRIP), where large spikes in electric field across the thylakoid membrane (Δψ) induce photosystem II recombination reactions that produce damaging singlet oxygen (1O2). Both qE and FRIP are directly linked to the thylakoid proton motive force (pmf), and in particular, the slow kinetics of partitioning pmf into its ΔpH and Δψ components. Using a series of computational simulations, we explored the possibility of ‘hacking' pmf partitioning as a target for improving photosynthesis. Under a range of illumination conditions, increasing the rate of counter-ion fluxes across the thylakoid membrane should lead to more rapid dissipation of Δψ and formation of ΔpH. This would result in increased rates for the formation and decay of qE while resulting in a more rapid decline in the amplitudes of Δψ-spikes and decreasing 1O2 production. These results suggest that ion fluxes may be a viable target for plant breeding or engineering. However, these changes also induce transient, but substantial mismatches in the ATP : NADPH output ratio as well as in the osmotic balance between the lumen and stroma, either of which may explain why evolution has not already accelerated thylakoid ion fluxes. Overall, though the model is simplified, it recapitulates many of the responses seen in vivo, while spotlighting critical aspects of the complex interactions between pmf components and photosynthetic processes. By making the programme available, we hope to enable t
Kornienko N, van Grondelle R, Rutherford AW, et al., 2017, Quantitatively probing photosystem II with a rotating ring disk electrode assembly, 254th National Meeting and Exposition of the American-Chemical-Society (ACS) on Chemistry's Impact on the Global Economy, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Kaucikas M, Nurnberg D, Dorhliac G, et al., 2017, Femtosecond visible transient absorption spectroscopy ofChlorophyll f-containing Photosystem I, Biophysical Journal, Vol: 112, Pages: 234-249, ISSN: 1542-0086
Photosystem I (PSI) from Chroococcidiopsis thermalis PCC 7203 grown under far-red light (FRL; >725 nm) contains both chlorophyll a and a small proportion of chlorophyll f. Here, we investigated excitation energy transfer and charge separation using this FRL-grown form of PSI (FRL-PSI). We compared femtosecond transient visible absorption changes of normal, white-light (WL)-grown PSI (WL-PSI) with those of FRL-PSI using excitation at 670 nm, 700 nm, and (in the case of FRL-PSI) 740 nm. The possibility that chlorophyll f participates in energy transfer or charge separation is discussed on the basis of spectral assignments. With selective pumping of chlorophyll f at 740 nm, we observe a final ∼150 ps decay assigned to trapping by charge separation, and the amplitude of the resulting P700+•A1−• charge-separated state indicates that the yield is directly comparable to that of WL-PSI. The kinetics shows a rapid 2 ps time constant for almost complete transfer to chlorophyll f if chlorophyll a is pumped with a wavelength of 670 nm or 700 nm. Although the physical role of chlorophyll f is best supported as a low-energy radiative trap, the physical location should be close to or potentially within the charge-separating pigments to allow efficient transfer for charge separation on the 150 ps timescale. Target models can be developed that include a branching in the formation of the charge separation for either WL-PSI or FRL-PSI.
Rutherford AW, Fantuzzi A, Brinkert K, et al., 2016, Bicarbonate-induced redox tuning in Photosystem II for regulation and protection, Proceedings of the National Academy of Sciences of the United States of America, Vol: 113, Pages: 12144-12149, ISSN: 1091-6490
The midpoint potential (Em) of QA/Q−∙AQA/QA−•, the one-electron acceptor quinone of Photosystem II (PSII), provides the thermodynamic reference for calibrating PSII bioenergetics. Uncertainty exists in the literature, with two values differing by ∼80 mV. Here, we have resolved this discrepancy by using spectroelectrochemistry on plant PSII-enriched membranes. Removal of bicarbonate (HCO3−) shifts the Em from ∼−145 mV to −70 mV. The higher values reported earlier are attributed to the loss of HCO3− during the titrations (pH 6.5, stirred under argon gassing). These findings mean that HCO3− binds less strongly when QA−• is present. Light-induced QA−• formation triggered HCO3− loss as manifest by the slowed electron transfer and the upshift in the Em of QA. HCO3−-depleted PSII also showed diminished light-induced 1O2 formation. This finding is consistent with a model in which the increase in the Em of QA/Q−∙AQA/QA−• promotes safe, direct P+∙Q−∙AP+•QA−• charge recombination at the expense of the damaging back-reaction route that involves chlorophyll triplet-mediated 1O2 formation [Johnson GN, et al. (1995) Biochim Biophys Acta 1229:202–207]. These findings provide a redox tuning mechanism, in which the interdependence of the redox state of QA and the binding by HCO3− regulates and protects PSII. The potential for a sink (CO2) to source (PSII) feedback mechanism is discussed.
Davis GA, Kanazawa A, Schöttler MA, et al., 2016, Limitations to photosynthesis by proton motive force-induced photosystem II photodamage., eLife, Vol: 5, ISSN: 2050-084X
The thylakoid proton motive force (pmf) generated during photosynthesis is the essential driving force for ATP production; it is also a central regulator of light capture and electron transfer. We investigated the effects of elevated pmf on photosynthesis in a library of Arabidopsis thaliana mutants with altered rates of thylakoid lumen proton efflux, leading to a range of steady-state pmf extents. We observed the expected pmf-dependent alterations in photosynthetic regulation, but also strong effects on the rate of photosystem II (PSII) photodamage. Detailed analyses indicate this effect is related to an elevated electric field (Δψ) component of the pmf, rather than lumen acidification, which in vivo increased PSII charge recombination rates, producing singlet oxygen and subsequent photodamage. The effects are seen even in wild type plants, especially under fluctuating illumination, suggesting that Δψ-induced photodamage represents a previously unrecognized limiting factor for plant productivity under dynamic environmental conditions seen in the field.
Brinkert K, Le formal F, Li X, et al., 2016, Photocurrents from photosystem II in a metal oxide hybrid system: electron transfer pathways, Biochimica et Biophysica Acta-Bioenergetics, Vol: 1857, Pages: 1497-1505, ISSN: 0005-2728
We have investigated the nature of the photocurrent generated by Photosystem II (PSII), the water oxidising enzyme, isolated from Thermosynechococcus elongatus, when immobilized on nanostructured titanium dioxide on an indium tin oxide electrode (TiO2/ITO). We investigated the properties of the photocurrent from PSII when immobilized as a monolayer versus multilayers, in the presence and absence of an inhibitor that binds to the site of the exchangeable quinone (QB) and in the presence and absence exogenous mobile electron carriers (mediators). The findings indicate that electron transfer occurs from the first quinone (QA) directly to the electrode surface but that the electron transfer through the nanostructured metal oxide is the rate-limiting step. Redox mediators enhance the photocurrent by taking electrons from the nanostructured semiconductor surface to the ITO electrode surface not from PSII. This is demonstrated by photocurrent enhancement using a mediator incapable of accepting electrons from PSII. This model for electron transfer also explains anomalies reported in the literature using similar and related systems. The slow rate of the electron transfer step in the TiO2 is due to the energy level of electron injection into the semiconducting material being below the conduction band. This limits the usefulness of the present hybrid electrode. Strategies to overcome this kinetic limitation are discussed.
Rutherford AW, Prell J, MacKellar D, et al., 2016, Streptomyces thermoautotrophicus does not fix nitrogen, Scientific Reports, Vol: 6, ISSN: 2045-2322
Streptomyces thermoautotrophicus UBT1 has been described as a moderately thermophilic chemolithoautotroph with a novel nitrogenase enzyme that is oxygen-insensitive. We have cultured the UBT1 strain, and have isolated two new strains (H1 and P1-2) of very similar phenotypic and genetic characters. These strains show minimal growth on ammonium-free media, and fail to incorporate isotopically labeled N2 gas into biomass in multiple independent assays. The sdn genes previously published as the putative nitrogenase of S. thermoautotrophicus have little similarity to anything found in draft genome sequences, published here, for strains H1 and UBT1, but share >99% nucleotide identity with genes from Hydrogenibacillus schlegelii, a draft genome for which is also presented here. H. schlegelii similarly lacks nitrogenase genes and is a non-diazotroph. We propose reclassification of the species containing strains UBT1, H1, and P1-2 as a non-Streptomycete, non-diazotrophic, facultative chemolithoautotroph and conclude that the existence of the previously proposed oxygen-tolerant nitrogenase is extremely unlikely.
Ugur I, Rutherford AW, Kaila VR, 2016, Redox-coupled substrate water reorganization in the active site of Photosystem II - the role of calcium in substrate water delivery, Biochimica et Biophysica Acta - Bioenergetics, Vol: 1857, Pages: 740-748, ISSN: 0005-2728
Photosystem II (PSII) catalyzes light-driven water splitting in nature and is the key enzyme for energy input into the biosphere. Important details of its mechanism are not well understood. In order to understand the mechanism of water splitting, we perform here large-scale density functional theory (DFT) calculations on the active site of PSII in different oxidation, spin and ligand states. Prior to formation of the O-O bond, we find that all manganese atoms are oxidized to Mn(IV) in the S3 state, consistent with earlier studies. We find here, however, that the formation of the S3 state is coupled to the movement of a calcium-bound hydroxide (W3) from the Ca to a Mn (Mn1 or Mn4) in a process that is triggered by the formation of a tyrosyl radical (Tyr-161) and its protonated base, His-190. We find that subsequent oxidation and deprotonation of this hydroxide on Mn1 result in formation of an oxyl-radical that can exergonically couple with one of the oxo-bridges (O5), forming an O-O bond. When O2 leaves the active site, a second Ca-bound water molecule reorients to bridge the gap between the manganese ions Mn1 and Mn4, forming a new oxo-bridge for the next reaction cycle. Our findings are consistent with experimental data, and suggest that the calcium ion may control substrate water access to the water oxidation sites.
Saito K, Rutherford AW, Ishikita H, 2015, Energetics of proton release on the first oxidation step in the water-oxidizing enzyme, Nature Communications, Vol: 6, ISSN: 2041-1723
In photosystem II (PSII), the Mn4CaO5 cluster catalyses the water splitting reaction. The crystal structure of PSII shows the presence of a hydrogen-bonded water molecule directly linked to O4. Here we show the detailed properties of the H-bonds associated with the Mn4CaO5 cluster using a quantum mechanical/molecular mechanical approach. When O4 is taken as a μ-hydroxo bridge acting as a hydrogen-bond donor to water539 (W539), the S0 redox state best describes the unusually short O4–OW539 distance (2.5 Å) seen in the crystal structure. We find that in S1, O4 easily releases the proton into a chain of eight strongly hydrogen-bonded water molecules. The corresponding hydrogen-bond network is absent for O5 in S1. The present study suggests that the O4-water chain could facilitate the initial deprotonation event in PSII. This unexpected insight is likely to be of real relevance to mechanistic models for water oxidation.
Mersch D, Lee C-Y, Zhang JZ, et al., 2015, Wiring of Photosystem II to Hydrogenase for Photoelectrochemical Water Splitting, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 137, Pages: 8541-8549, ISSN: 0002-7863
Boussac A, Rutherford AW, Sugiura M, 2015, Electron transfer pathways from the S-2-states to the S-3-states either after a Ca2+/Sr2+ or a Cl-/I- exchange in Photosystem II from, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, Vol: 1847, Pages: 576-586, ISSN: 0005-2728
Cardona Londono T, Murray JW, Rutherford AW, 2015, Origin and evolution of water oxidation before the last common ancestor of the Cyanobacteria, Molecular Biology and Evolution, ISSN: 1537-1719
Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster (Mn4CaO5) of Photosystem II. We show that D1 exists in several forms making well-defined clades, some of which could have evolved before the origin of water oxidation and presenting many atypical characteristics. The most ancient form is found in the genome of Gloeobacter kilaueensis JS-1 and this has a C-terminus with a higher sequence identity to D2 than to any other D1. Two other groups of early evolving D1 correspond to those expressed under prolonged far-red illumination and in darkness. These atypical D1 forms are characterized by a dramatically different Mn4CaO5 binding site and a Photosystem II containing such a site may assemble an unconventional metal cluster. The first D1 forms with a full set of ligands to the Mn4CaO5 cluster are grouped with D1 proteins expressed only under low oxygen concentrations and the latest evolving form is the dominant type of D1 found in all cyanobacteria and plastids. In addition, we show that the plastid ancestor had a D1 more similar to those in early branching Synechococcus. We suggest each one of these forms of D1 originated from transitional forms at different stages towards the innovation and optimization of water oxidation before the last common ancestor of all known cyanobacteria.
Rutherford AW, 2014, Redox tuning in biological electron transfer: sacrificing efficiency to survive life in O-2, 12th European Biological Inorganic Chemistry Conference (EuroBIC), Publisher: SPRINGER, Pages: S704-S704, ISSN: 0949-8257
Sugiura M, Azami C, Koyama K, et al., 2014, Modification of the pheophytin redox potential in Therrnosynechococcus elongatus Photosystem II with PsbA3 as D1, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, Vol: 1837, Pages: 139-148, ISSN: 0005-2728
Kato M, Cardona T, Rutherford AW, et al., 2013, Covalent Immobilization of Oriented Photosystem II on a Nanostructured Electrode for Solar Water Oxidation, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 135, Pages: 10610-10613, ISSN: 0002-7863
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.