Density functional calculations modelling tyrosine oxidation in oxygenic photosynthetic electron transfer

Hybrid density functional calculations are used to model tyrosine oxidation during electron transfer reactions of photosystem II. The predicted frequency values for the 7a and deltaCOH modes of the reduced form and the 7a mode of the oxidised radical form are in excellent agreement with experimental data obtained for Mn and Ca depleted systems by Hienerwadel et al. [Biochemistry 36 (1997) 15447] and Berthomieu et al. [Biochemistry 37 (1998) 10547]. The calculations confirm that the two tyrosines Y(D) and Y(Z) are protonated in the reduced form. On oxidation the larger 7a frequency value observed experimentally for Y(Z*) can be best explained by a greater localisation of the protonic charge released on formation of this tyrosyl free radical.     

A hydrogen-atom abstraction model for the function of YZ in photosynthetic oxygen evolution

Recent magnetic-resonance work on Y suggests that this species exhibits considerable motional flexibility in its functional site and that its phenol oxygen is not involved in a well-ordered hydrogen-bond interaction (Tang et al., submitted; Tommos et al., in press). Both of these observations are inconsistent with a simple electron-transfer function for this radical in photosynthetic water oxidation. By considering the roles of catalytically active amino acid radicals in other enzymes and recent data on the water-oxidation process in Photosystem II, we rationalize these observations by suggesting that Y functions to abstract hydrogen atoms from aquo- and hydroxy-bound managanese ions in the (Mn)₄ cluster on each S-state transition. The hydrogen-atom abstraction process may occur either by sequential or concerted kinetic pathways. Within this model, the (Mn)₄/Y_Z center forms a single catalytic center that comprises the Oxygen Evolving Complex in Photosystem II.     

A carboxylic residue at the high-affinity, Mn-binding site participates in the binding of iron cations that block the site

The role of carboxylic residues at the high-affinity, Mn-binding site in the ligation of iron cations blocking the site [Biochemistry 41 (2000) 5854] was studied, using a method developed to extract the iron cations blocking the site. We found that specifically bound Fe(III) cations can be extracted with citrate buffer at pH 3.0. Furthermore, citrate can also prevent the photooxidation of Fe(II) cations by Y_Z. Participation of a COOH group(s) in the ligation of Fe(III) at the high-affinity site was investigated using 1-ethyl-3-[(3-dimethylamino)propyl] carbodiimide (EDC), a chemical modifier of carboxylic amino acid residues. Modification of the COOH groups inhibits the light-induced oxidation of exogenous Mn(II) cations by Mn-depleted photosystem II (PSII[−Mn]) membranes. The rate of Mn(II) oxidation saturates at ≥10 μM in PSII(−Mn) membranes and ≥500 μM in EDC-treated PSII (−Mn) samples. Intact PSII(−Mn) membranes have only one site for Mn(II) oxidation via Y_Z (dissociation constant, K_d = 0.64 μM), while EDC-treated PSII(−Mn) samples have two sites (K_d = 1.52 and 22 μM; the latter is the low-affinity site). When PSII(−Mn) membranes were incubated with Fe(II) before modifier treatment (to block the high-affinity site) and the blocking iron cations were extracted with citrate (pH 3.0) after modification, the membranes contained only one site (K_d = 2.3 μM) for exogenous Mn(II) oxidation by Y_Z radical. In this case, the rate of electron donation via Y_Z saturated at a Mn(II) concentration ≥15 μM. These results indicate that the carboxylic residue participating in Mn(II) coordination and the binding of oxidized manganese cations at the HA_Z site is protected from the action of the modifier by the iron cations blocking the HA_Z site. We concluded that the carboxylic residue (D1 Asp-170) participating in the coordination of the manganese cation at the HA_Z site (Mn4 in the tetranuclear manganese cluster [Science 303 (2004) 1831]) is also involved in the ligation of the Fe cation(s) blocking the high-affinity Mn-binding site.     

Molecular origin of the pH dependence of tyrosine D oxidation kinetics and radical stability in photosystem II

A role for redox-active tyrosines has been demonstrated in many important biological processes, including water oxidation carried out by photosystem II (PSII) of oxygenic photosynthesis. The rates of tyrosine oxidation and reduction and the Tyr/Tyr reduction potential are undoubtedly controlled by the immediate environment of the tyrosine, with the coupling of electron and proton transfer, a critical component of the kinetic and redox behavior. It has been demonstrated by Faller et al. that the rate of oxidation of tyrosine D (Tyr_D) at room temperature and the extent of Tyr_D oxidation at cryogenic temperatures, following flash excitation, dramatically increase as a function of pH with a pK_a of ≈ 7.6 [Faller et al. 2001 Proc. Natl. Acad. Sci. USA 98, 14368-14373; Faller et al. 2001 Biochemistry 41, 12914-12920]. In this work, we investigated, using FTIR difference spectroscopy, the mechanistic reasons behind this large pH dependence. These studies were carried out on Mn-depleted PSII core complexes isolated from Synechocystis sp. PCC 6803, WT unlabeled and labeled with ¹³C₆-, or ¹³C₁(4)-labeled tyrosine, as well as on the D2-Gln164Glu mutant. The main conclusions of this work are that the pH-induced changes involve the reduced Tyr_D state and not the oxidized Tyr_D state and that Tyr_D does not exist in the tyrosinate form between pH 6 and 10. We can also exclude a change in the protonation state of D2-His189 as being responsible for the large pH dependence of Tyr_D oxidation. Indeed, our data are consistent with D2-His189 being neutral both in the Tyr_D and Tyr_D states in the whole pH6-10 range. We show that the interactions between reduced Tyr_D and D2-His189 are modulated by the pH. At pH greater than 7.5, the ν(CO) mode frequency of Tyr_D indicates that Tyr_D is involved in a strong hydrogen bond, as a hydrogen bond donor only, in a fraction of the PSII centers. At pH below 7.5, the hydrogen-bonding interaction formed by Tyr_D is weaker and Tyr_D could be also involved as a hydrogen bond acceptor, according to calculations performed by Takahashi and Noguchi [J. Phys. Chem. B 2007 111, 13833-13844]. The involvement of Tyr_D in this strong hydrogen-bonding interaction correlates with the ability to oxidize Tyr_D at cryogenic temperatures and rapidly at room temperature. A strong hydrogen-bonding interaction is also observed at pH 6 in the D2-Gln164Glu mutant, showing that the residue at position D2-164 regulates the properties of Tyr_D. The IR data point to the role of a protonatable group(s) (with a pK_a of ≈ 7) other than D2-His189 and Tyr_D, in modifying the characteristics of the Tyr_D hydrogen-bonding interactions, and hence its oxidation properties. It remains to be determined whether the strong hydrogen-bonding interaction involves D2-His189 and if Tyr_D oxidation involves the same proton transfer route at low and at high pH.     

EPR properties of a g=2 broad signal trapped in an S1 state in Ca-depleted Photosystem II

We investigated a new EPR signal that gives a broad line shape around g=2 in Ca²⁺-depleted Photosystem (PS) II. The signal was trapped by illumination at 243 K in parallel with the formation of Y_Z. The ratio of the intensities between the g=2 broad signal and the Y_Z signal was 1:3, assuming a Gaussian line shape for the former. The g=2 broad signal and the Y_Z signal decayed together in parallel with the appearance of the S₂ state multiline at 243 K. The g=2 broad signal was assigned to be an intermediate S₁X state in the transition from the S₁ to the S₂ state, where X represents an amino acid radical nearby manganese cluster, such as D1-His337. The signal is in thermal equilibrium with Y_Z. Possible reactions in the S state transitions in Ca²⁺-depleted PS II were discussed.     

Photoproduction of the Azidyl Radical from the Azide Anion on the Oxidizing Side of Photosystem II and Suppression of Photooxidation of Tyrosine Z by the Azidyl Radical

Azide ions inhibited O₂ evolution in PSII membranes from spinachin a time-dependent manner in the light until all activity disappeared.Illumination in the presence of azide (azide-phototreatment)irreversibly inhibited the following processes: (1) both theoxidation of water and the electron transport between the redox-activetyrosine 161 of the D1 protein (Y_Z) and the secondary quinoneelectron acceptor (Q_B) site, to the same extent; (2) the donationof electrons to the primary quinone electron acceptor (Q_A),as measured by monitoring the maximum variable fluorescenceof Chl; and (3) the photoproduction of the Y_Z radical (Y). Thus,the primary site of inhibition appeared to lie between Y_Z andQ_A. On illumination of Tris-treated PSII membranes in the presenceof azide, production of the azidyl radical was observed by spin-trappingESR. Yield of Y in Tris-treated membranes on illumination wassuppressed by azide. Electron transport from Y_Z to Q_B in Tris-treatedmembranes was inhibited only when the azidyl radical was photoproduced,and it was inhibited more rapidly than it was in the oxygenicPSII membranes. These results indicate that the azidyl radicalwas produced via a univalent oxidation of azide by Y and thatit irreversibly inhibited the electron transport from Y_Z toQ_A in Tris-treated membranes. Although the azidyl radical wasundetectable in the oxygenic PSII membranes, probably due tosteric interference by the peripheral proteins of water-oxidizingcomplex with the access of the spin-trapping reagent to theproduction site of the radical, the participation of the azidylradical in the inhibition of the oxygenic PSII membranes issuggested since simultaneous occurrence of both electron transportand azide was required for the inhibition. Possible inhibitorymechanisms and the target sites of azidyl radical are discussed. (Received April 21, 1995; Accepted July 3, 1995)     

A proposed role for inorganic carbon in water oxidation

This is an article on the peroxydicarbonic acid (PODCA) hypothesis of photosynthetic water oxidation, which follows our first article in this general area (Castelfranco et al., Photosynth Res 94:235–246, 2007). In this article I have expanded on the idea of a protein-bound intermediate containing inorganic carbon in some chemically bound form. PODCA is conceived in this article as constituting a bridge between two proteins of the oxygen-evolving complex (OEC) that are essential for the evolution of O₂. Presumably, these are two proteins which have been shown to possess Mn-dependent carbonic anhydrase activity (Lu et al., Plant Cell Physiol 46:1944–1953, 2005; Shitov et al., Biochemistry (Moscow) 74:509–517, 2009). One of these proteins may be the D_I of the OEC core and the other may be the PsbO extrinsic protein. I attempt to relate briefly the PODCA hypothesis to the role of two cofactors for O₂ evolution: Ca²⁺ and inorganic carbon. In this scheme, inorganic carbon (HCO₃ ^?) mediates the oxidation of peroxide to dioxygen, thus avoiding the homolytic cleavage of the peroxide into two free radicals. I visualize the role of Ca²⁺ in the binding of PODCA to two essential photosystem II proteins. I propose that PODCA alternates between two Phases. In Phase 1, PODCA is broken down with the production of O₂. In Phase 2, PODCA is regenerated.     

EPR kinetic studies of the S−1 state in spinach thylakoids

The Y_Z decay kinetics in a formal S₋₁ state, regarded as a reduced state of the oxygen evolving complex, was determined using time-resolved EPR spectroscopy. This S₋₁ state was generated by biochemical treatment of thylakoid membranes with hydrazine. The steady-state oxygen evolution of the sample was used to optimize the biochemical procedure for performing EPR experiments. A high yield of the S₋₁ state was generated as judged by the two-flash delay in the first maximum of oxygen evolution in Joliot flash-type experiments. We have shown that the Y_Z re-reduction rate by the S₋₁ state is much slower than that of any other S-state transition in hydrazine-treated samples. This slow reduction rate in the S₋₁ to S₀ transition, which is in the order of the S₃ to S₀ transition rate, suggests that this transition is accompanied by some structural rearrangements. Possible explanations of this unique, slow reduction rate in the S₋₁ to S₀ transition are considered, in light of earlier observations by others on hydrazine/hydroxylamine reduced PS II samples.     

Decay Kinetics of Tyrosine Radical (YZ •) in Chloride Anion-Depleted Photosystem 2 Studied by Time-Resolved EPR

The decay of tyrosine cation radical was found to be biphasic at 253 K. The fast phase corresponds to the Y_Z component while the slow phase corresponds to the tyrosine D radical (Y_D ) component. At 253 K, the t_1/2 value was 28.6 s for the fast phase and 190.7 s for the slow phase. The fast phase is attributed to the recombination of charges between Y_Z and Q_A ^–. The activation energy for the reaction of Y_Z with Q_A ^– between 253 and 293 K was 48 kJ mol^–1 in Cl^–-depleted photosystem 2 (PS2) membranes. Both the decay rate and the amplitude of the PAR -induced signal of Y_Z were affected by addition of chloride anion. Change in the decay rate and the amplitude of the PAR-induced signal of Y_Z was observed when other anions like Br^–, I^–, F, HCO₃ ^–, NO₃ ^–, PO₄ ^3– were substituted in the Cl^–-depleted PS2.     

Acceptor side effects on the electron transfer at cryogenic temperatures in intact photosystem II

In intact PSII, both the secondary electron donor (Tyr_Z) and side-path electron donors (Car/Chl_Z/Cyt_b559) can be oxidized by P₆₈₀⁺ at cryogenic temperatures. In this paper, the effects of acceptor side, especially the redox state of the non-heme iron, on the donor side electron transfer induced by visible light at cryogenic temperatures were studied by EPR spectroscopy. We found that the formation and decay of the S₁Tyr_Z EPR signal were independent of the treatment of K₃Fe(CN)₆, whereas formation and decay of the Car⁺/Chl_Z⁺ EPR signal correlated with the reduction and recovery of the Fe³⁺ EPR signal of the non-heme iron in K₃Fe(CN)₆ pre-treated PSII, respectively. Based on the observed correlation between Car/Chl_Z oxidation and Fe³⁺ reduction, the oxidation of non-heme iron by K₃Fe(CN)₆ at 0 °C was quantified, which showed that around 50-60% fractions of the reaction centers gave rise to the Fe³⁺ EPR signal. In addition, we found that the presence of phenyl-p-benzoquinone significantly enhanced the yield of Tyr_Z oxidation. These results indicate that the electron transfer at the donor side can be significantly modified by changes at the acceptor side, and indicate that two types of reaction centers are present in intact PSII, namely, one contains unoxidizable non-heme iron and another one contains oxidizable non-heme iron. Tyr_Z oxidation and side-path reaction occur separately in these two types of reaction centers, instead of competition with each other in the same reaction centers. In addition, our results show that the non-heme iron has different properties in active and inactive PSII. The oxidation of non-heme iron by K₃Fe(CN)₆ takes place only in inactive PSII, which implies that the Fe³⁺ state is probably not the intermediate species for the turnover of quinone reduction.     

A Signaling Pathway Linking Nitric Oxide Production to Heterotrimeric G Protein and Hydrogen Peroxide Regulates Extracellular Calmodulin Induction of Stomatal Closure in Arabidopsis

Extracellular calmodulin (ExtCaM) regulates stomatal movement by eliciting a cascade of intracellular signaling events including heterotrimeric G protein, hydrogen peroxide (H₂O₂), and Ca²⁺. However, the ExtCaM-mediated guard cell signaling pathway remains poorly understood. In this report, we show that Arabidopsis (Arabidopsis thaliana) NITRIC OXIDE ASSOCIATED1 (AtNOA1)-dependent nitric oxide (NO) accumulation plays a crucial role in ExtCaM-induced stomatal closure. ExtCaM triggered a significant increase in NO levels associated with stomatal closure in the wild type, but both effects were abolished in the Atnoa1 mutant. Furthermore, we found that ExtCaM-mediated NO generation is regulated by GPA1, the Gα-subunit of heterotrimeric G protein. The ExtCaM-dependent NO accumulation was nullified in gpa1 knockout mutants but enhanced by overexpression of a constitutively active form of GPA1 (cGα). In addition, cGα Atnoa1 and gpa1-2 Atnoa1 double mutants exhibited a similar response as did Atnoa1. The defect in gpa1 was rescued by overexpression of AtNOA1. Finally, we demonstrated that G protein activation of NO production depends on H₂O₂. Reduced H₂O₂ levels in guard cells blocked the stomatal response of cGα lines, whereas exogenously applied H₂O₂ rescued the defect in ExtCaM-mediated stomatal closure in gpa1 mutants. Moreover, the atrbohD/F mutant, which lacks the NADPH oxidase activity in guard cells, had impaired NO generation in response to ExtCaM, and H₂O₂-induced stomatal closure and NO accumulation were greatly impaired in Atnoa1. These findings have established a signaling pathway leading to ExtCaM-induced stomatal closure, which involves GPA1-dependent activation of H₂O₂ production and subsequent AtNOA1-dependent NO accumulation.Plant guard cells control opening and closure of the stomata in response to phytohormones (e.g. abscisic acid [ABA]) and various environmental signals such as light and temperature, thereby regulating gas exchange for photosynthesis and water status via transpiration (Schroeder et al., 2001). Cytosolic calcium ([Ca²⁺]_i) has been shown to be a key second messenger that changes in response to multiple stimuli in guard cells (McAinsh et al., 1995; Grabov and Blatt, 1998; Wood et al., 2000). A large proportion of Ca²⁺ is localized in extracellular space. It has been shown that external Ca²⁺ concentration ([Ca²⁺]_o) promotes stomatal closure and induces oscillation in [Ca²⁺]_i in guard cells (MacRobbie, 1992; McAinsh et al., 1995; Allen et al., 2001). However, how the guard cells perceive [Ca²⁺]_o concentration and convert [Ca²⁺]_o changes into [Ca²⁺]_i changes was not understood until a calcium-sensing receptor (CAS) in the plasma membrane of guard cells in Arabidopsis (Arabidopsis thaliana) was identified (Han et al., 2003). The external Ca²⁺ (Ca²⁺_o)-induced [Ca²⁺]_i increase is abolished in CAS antisense lines (Han et al., 2003). Both [Ca²⁺]_o and [Ca²⁺]_i show diurnal oscillation that is determined by stomatal conductance, whereas the amplitude of [Ca²⁺]_i oscillation is reduced in CAS antisense lines (Tang et al., 2007). The reduced amplitude of [Ca²⁺]_i diurnal oscillation in response to Ca²⁺_o treatment suggests the potential existence of other [Ca²⁺]_o sensor(s) that may transmit [Ca²⁺]_o information into the [Ca²⁺]_i response in coordination with CAS. Extracellular calmodulin (ExtCaM) could be such an additional [Ca²⁺]_o sensor.Calmodulin is a well-known Ca²⁺ sensor that is activated upon binding of Ca²⁺. It has been shown that calmodulin exists not only intracellularly but also extracellularly in many plant species (Biro et al., 1984; Sun et al., 1994, 1995; Cui et al., 2005). ExtCaM has been implicated in several important biological functions, such as the promotion of cell proliferation, pollen germination, and tube growth (Sun et al., 1994, 1995; Ma and Sun, 1997; Ma et al., 1999; Cui et al., 2005; Shang et al., 2005). ExtCaM is found in the cell wall of guard cells in Vicia faba and in the epidermis of Arabidopsis by immunogold labeling/electron microscopy and western-blot analyses, respectively, and the endogenous CaM in the extracellular space has been shown to regulate stomatal movements (Chen et al., 2003; Xiao et al., 2004). Under natural conditions, once the activity of ExtCaM has been inhibited by its membrane-impermeable antagonist W7-agrose or CaM antibody, stomatal opening under light is enhanced and stomatal closure in darkness is inhibited in V. faba and Arabidopsis (Chen et al., 2003; Xiao et al., 2004). [Ca²⁺]_i and cytosolic hydrogen peroxide (H₂O₂) changes, two events involved in ExtCaM-regulated stomatal movement (Chen et al., 2004), are likely regulated by light/darkness (Chen and Gallie, 2004; Tang et al., 2007), suggesting that ExtCaM plays an important physiological role in the regulation of stomatal diurnal rhythm. Calmodulin-binding proteins have been found in the protoplast of suspension-cultured Arabidopsis cells, supporting the idea that ExtCaM functions as a peptide-signaling molecule (Cui et al., 2005). Furthermore, ExtCaM triggers [Ca²⁺]_i elevation in guard cells of V. faba and Arabidopsis and in lily (Lilium daviddi) pollen (Chen et al., 2004; Xiao et al., 2004; Shang et al., 2005). These observations support the notion that ExtCaM could be a potential [Ca²⁺]_o sensor for external calcium, and this external calcium sensing could subsequently regulate the [Ca²⁺]_i level through a signaling cascade.It is interesting that ExtCaM and ABA induce some parallel changes in second messengers in guard cell signaling. Our previous studies show that ExtCaM induces [Ca²⁺]_i increase and H₂O₂ generation through the Gα-subunit (GPA1) of a heterotrimeric G protein, and increased H₂O₂ further elevates [Ca²⁺]_i (Chen et al., 2004). G protein, Ca²⁺, and H₂O₂ are well-known second messengers in ABA-induced guard cell signaling (McAinsh et al., 1995; Grabov and Blatt, 1998; Pei et al., 2000; Wang et al., 2001; Zhang et al., 2001; Liu et al., 2007). However, the signaling cascade triggered by ExtCaM in guard cells is poorly understood. New ABA signaling components in guard cells could provide a clue in the study of the molecular mechanism of ExtCaM guard cell signaling.Recently, nitric oxide (NO) has been shown to serve as an important signal molecule involved in many aspects of developmental processes, including floral transition, root growth, root gravitropism, adventitious root formation, xylogenesis, seed germination, and orientation of pollen tube growth (Beligni and Lamattina, 2000; Pagnussat et al., 2002; He et al., 2004; Prado et al., 2004; Gabaldón et al., 2005; Stohr and Stremlau, 2006). Increasing evidence points to a role for NO as an essential component in ABA signaling in guard cells (Garcia-Mata and Lamattina, 2001, 2002; Neill et al., 2002). It has been shown that nitrate reductase (NR) reduces nitrite to NO, and the nia1, nia2 NR-deficient mutant in Arabidopsis showed reduced ABA induction of stomatal closure (Desikan et al., 2002; Bright et al., 2006). Although animal nitric oxide synthase (NOS) activity has been detected in plants and inhibitors of mammalian NOS impair NO production in plants (Barroso et al., 1999; Corpas et al., 2001), the gene(s) encoding NOS in plants is still not clear. AtNOS1 in Arabidopsis was initially reported to encode a protein containing NOS activity (Guo et al., 2003). However, recent studies have raised critical questions regarding the nature of AtNOS1 and suggested that AtNOS1 appears not to encode a NOS (Crawford et al., 2006; Zemojtel et al., 2006). However, the originally described Atnos1 mutant is deficient in NO accumulation (Crawford et al., 2006). Consequently, AtNOS1 was renamed AtNOA1 (for NITRIC OXIDE ASSOCIATED1; Crawford et al., 2006). Therefore, the Atnoa1 mutant provides a useful tool for dissecting the function of NO in plants. At present, the molecules that regulate NO generation in ABA-mediated guard cell signaling are not clear. Evidence suggests that H₂O₂, a second messenger important for the regulation of many developmental processes and stomatal movement (Pei et al., 2000; Zhang et al., 2001; Coelho et al., 2002; Demidchik et al., 2003; Kwak et al., 2003), regulates NO generation in guard cells (Lum et al., 2002; He et al., 2005; Bright et al., 2006).Given the parallel signaling events induced by ABA and ExtCaM, we investigated whether NO is involved in the regulation of ExtCaM-induced stomatal closure in Arabidopsis and whether it is linked to G protein and H₂O₂, two key regulators of both ExtCaM and ABA regulation of stomatal movements. Using Arabidopsis mutants (e.g. GPA1 null mutants, the NO-producing mutant Atnoa1, and the guard cell H₂O₂ synthetic enzymatic mutant atrbohD/F) combined with pharmacological analysis, we present compelling evidence to establish a linear functional relationship between Gα, H₂O₂, and NO in ExtCaM guard cell signaling.     

Overview on Peroxiredoxin

Peroxiredoxins (Prxs) are a very large and highly conserved family of peroxidases that reduce peroxides, with a conserved cysteine residue, designated the “peroxidatic” Cys (C_P) serving as the site of oxidation by peroxides (Hall et al., 2011; Rhee et al., 2012). Peroxides oxidize the C_P-SH to cysteine sulfenic acid (C_P–SOH), which then reacts with another cysteine residue, named the “resolving” Cys (C_R) to form a disulfide that is subsequently reduced by an appropriate electron donor to complete a catalytic cycle. This overview summarizes the status of studies on Prxs and relates the following 10 minireviews.     

Centimeter-long electron transport in marine sediments via conductive minerals

Centimeter-long electron conduction through marine sediments, in which electrons derived from sulfide in anoxic sediments are transported to oxygen in surficial sediments, may have an important influence on sediment geochemistry. Filamentous bacteria have been proposed to mediate the electron transport, but the filament conductivity could not be verified and other mechanisms are possible. Surprisingly, previous investigations have never actually measured the sediment conductivity or its basic physical properties. Here we report direct measurements that demonstrate centimeter-long electron flow through marine sediments, with conductivities sufficient to account for previously estimated electron fluxes. Conductivity was lost for oxidized sediments, which contrasts with the previously described increase in the conductivity of microbial biofilms upon oxidation. Adding pyrite to the sediments significantly enhanced the conductivity. These results suggest that the role of conductive minerals, which are more commonly found in sediments than centimeter-long microbial filaments, need to be considered when modeling marine sediment biogeochemistry.To evaluate the conductivity of coastal anaerobic marine sediments, gold electrodes separated by a 50-μm nonconductive gap were inserted at different depths in intact sediment cores collected from Nantucket Bay, Massachusetts (Figure 1a). Conductivity of the sediments was measured with techniques comparable to those previously used to document the conductivity of microbial pili networks and biofilms (Malvankar et al., 2011, 2012a). This approach to measure in situ dc conductivity is substantially different from previous attempts to probe the conductivity of soils and sediments that either used self-potential monitoring (Ntarlagiannis et al., 2007) or measurements over small timescales (<1 s) (Regberg et al., 2011), which primarily measure the ionic contribution and not electron conductivity (Du et al., 2009; Patra et al., 2010). Direct conductivity measurements revealed values that were low in oxidized surficial sediments (<1 μS cm⁻¹); however, conductivities were significantly higher (P<0.05, t-test) in deeper, highly reduced sediments (Figure 1b). Along with intact sediment cores, experiments were also performed with mixed sediment subsamples. Comparable values of 7±0.15 μS cm⁻¹ (mean±s.e.; n=3) were obtained using this alternative approach, in which reduced sediments were placed on a four-probe electrode array under anaerobic conditions (Figure 1c) and conductivities measured over the 1-cm span of the electrodes.Open in a separate windowFigure 1Strategy to measure in situ sediment conductivity. (a) Schematic of setup to place intact cores of marine sediment. Gold electrodes with a 50-μm nonconductive spacing were inserted at different depths with respect to the overlying water. (b) Conductivity data of three independent sediment cores as a function of depth from the overlying water. Control setup was comprised of garden sand. Error bars represent s.d. These measurements were performed at 15 °C to mimic the physiological temperature of marine sediments. (c) Schematic of four-probe used to measure sediment conductivity. Current was injected using outer two gold electrodes and the voltage was measured using inner two gold electrodes using a high-impedance voltmeter.In previous studies (Nielsen et al., 2010) that led to the concept of long-range electron transport via conductive microbial filaments (Pfeffer et al., 2012), electric currents in the sediment were not actually measured, but rather inferred from rates of sediment oxygen consumption that were estimated from oxygen concentration profiles (Nielsen et al., 2010). In Aarhus Bay, estimated rates of oxygen consumption were 9.7 mmol O₂ per m² per day with 31% of this oxygen consumption attributed to electric current from deeper sediments (that is, 3 mmol O₂ per m² per day) and in Aarhus Harbor sediments 42% of the estimated 46 mmol O₂ per m² consumed per day (that is, 19.3 mmol O₂ per m² per day) was attributed to the inferred electric currents (Nielsen et al., 2010). Thus, given that four moles of electrons are required for each mole of oxygen reduced to water (O₂+4H⁺+4e⁻→2H₂O), the estimated electron flux through the sediments was 12–77 mmoles of electrons per m² per day. This electron flux through each m² of sediment can be converted to electric current as follows (calculations shown for maximum estimated flux): ((7.7 × 10⁻² moles of electrons per day) × (1.16 × 10⁻⁵ days s⁻¹) × (Amp/1.036 × 10⁻⁵ moles of electrons per second)=0.086 Amps or 86 mA for Aarhus Harbor sediments and 14 mA for the Aarhus Bay sediments). The proposed (Nielsen et al., 2010) reaction driving the electron flux is the oxidation of sulfide coupled to the reduction of oxygen, that is, a potential difference of ca. 1.1 V (HS⁻/S couple, −0.27 V; O₂/H₂O, +0.82 V; (Thauer et al., 1977)). The current (I) expected through 1 m² of sediment with the conductivity (σ) of 7 μS cm⁻¹ that was measured over 1 cm (approximate length of proposed conductive microbial filaments) of the Nantucket Bay sediments can be calculated from the relationship σ=G ×  l/A (l=length=1 cm; A=area=1 m² or 10⁴ cm²), where G is the conductance (G=I/V) and thus I=(V × A × σ)/l; (I=(1.1 V × 10⁴ cm² × 7 × 10⁻⁶ S cm⁻¹)/1 cm)=7.7 × 10⁻² V-S=77 mA. This compares well with the currents of 14–86 mA estimated from oxygen consumption in the sediments (Nielsen et al., 2010) in which it was proposed that microbial filaments were responsible for long-range electron transport (Pfeffer et al., 2012).To evaluate the contrast in conductivity between surficial oxidized sediments and deeper reduced sediments, reduced sediments were oxidized under air at 4 °C to preserve the biological components in the marine sediments such as bacterial c-type cytochromes and pili nanowires that have been hypothesized to confer conductivity to marine sediments (Nielsen et al., 2010; Reguera, 2012). Upon air-oxidation, conductivity of marine sediments declined ca. 90% (Figure 2a). Electrochemical oxidation of the sediments resulted in a similar conductivity loss (Figure 2b).Open in a separate windowFigure 2Effect of oxidation and mineral addition on sediment conductivity. (a) Effect of air-oxidation over days on the conductivity of marine sediments. Error bars represent s.d. (n=3 biological replicates). (b) Effect of electrochemical oxidation on the conductivity of marine sediments as a function of gate voltage using electrolyte-gated field-effect transistor geometry. (c) Effect of the addition of pyrite mineral to the conductivity of marine sediments. (d) Effect of the addition of pyrite mineral to the conductivity of freshwater sediments. All error bars represent s.d.The decrease in sediment conductivity upon oxidation contrasts with the two orders of magnitude increase in conductivity following oxidation of Geobacter sulfurreducens biofilms (Malvankar et al., 2011, 2012b), which are the only microbial system in which centimeter-long electron conduction has been directly documented. It is likely that oxidation increases conduction in G. sulfurreducens biofilms because the networks of pili that are thought to mediate long-range electron transport exhibit p-type conduction in which holes are majority carriers (Malvankar et al., 2011). The conductivity of p-type materials increases upon oxidation because the oxidation process increases the density of hole carriers (Heeger et al., 2010; Malvankar and Lovley, 2012). The suppression of sediment conductivity with oxidation indicated that long-range electron transport through the sediments is significantly different than that through G. sulfurreducens biofilms. It is unknown how oxidizing conditions might have an impact on the previously proposed conductivity through filamentous bacteria (Pfeffer et al., 2012; Malkin et al., 2014) because the hypothesized conductivity and the mechanisms for conduction have not been documented (Reguera, 2012).An abiological mechanism for electron transport through sediments that could potentially be eliminated with oxidation is conduction through iron–sulfur minerals. Dense assemblages of conductive iron–sulfur minerals in ore bodies (Sato and Mooney, 1960) or hydrothermal vents (Nakamura et al., 2010) may be capable of conducting electrons over distances of centimeters (Nakamura et al., 2010) to meters (Sato and Mooney, 1960). To determine whether lower abundances of an iron–sulfur mineral, comparable to those that might be found in reduced marine sediments, could contribute to conductivity, finely ground pyrite (10–100 μm diameters) was added to the reduced sediment. There was a significant increase in conductivity at higher pyrite concentrations (Figure 2c). The conductivity of freshwater sediment also increased upon addition of pyrite (Figure 2d).Although it has been suggested that filaments of cells closely related to Desulfobulbus species accounted for conductivity to reduced marine sediments from Aarhus Bay, it is, in fact, unknown whether this is possible because the conductivity of the filaments was not demonstrated (Pfeffer et al., 2012; Reguera, 2012; Malkin et al., 2014). No long bacterial filaments were observed in the Nantucket sediments used in these studies. The findings reported here, based on direct measurements of sediment conductivity, demonstrate that conductive minerals can confer substantial conductivity to anaerobic marine sediments and could potentially have an important role in sediment biogeochemistry. The simple method described here for assessing sediment conductivity is expected to be a useful tool for future studies of long-range electron conduction in a diversity of soils and sediments.     

Probing the role of Valine 185 of the D1 protein in the Photosystem II oxygen evolution

In Photosystem II (PSII), the Mn₄CaO₅-cluster of the active site advances through five sequential oxidation states (S₀ to S₄) before water is oxidized and O₂ is generated. The V185 of the D1 protein has been shown to be an important amino acid in PSII function (Dilbeck et al. Biochemistry 52 (2013) 6824–6833). Here, we have studied its role by making a V185T site-directed mutant in the thermophilic cyanobacterium Thermosynechococcus elongatus. The properties of the V185T-PSII have been compared to those of the WT*3-PSII by using EPR spectroscopy, polarography, thermoluminescence and time-resolved UV–visible absorption spectroscopy. It is shown that the V185 and the chloride binding site very likely interact via the H-bond network linking Tyr_Z and the halide. The V185 contributes to the stabilization of S₂ into the low spin (LS), S?=?1/2, configuration. Indeed, in the V185T mutant a high proportion of S₂ exhibits a high spin (HS), S?=?5/2, configuration. By using bromocresol purple as a dye, a proton release was detected in the S₁Tyr_Z?→?S₂^HSTyr_Z transition in the V185T mutant in contrast to the WT*3-PSII in which there is no proton release in this transition. Instead, in WT*3-PSII, a proton release kinetically much faster than the S₂^LSTyr_Z?→?S₃Tyr_Z transition was observed and we propose that it occurs in the S₂^LSTyr_Z?→?S₂^HSTyr_Z intermediate step before the S₂^HSTyr_Z?→?S₃Tyr_Z transition occurs. The dramatic slowdown of the S₃Tyr_Z?→?S₀Tyr_Z transition in the V185T mutant does not originate from a structural modification of the Mn₄CaO₅ cluster since the spin S?=?3?S₃ EPR signal is not modified in the mutant. More probably, it is indicative of the strong implication of V185 in the tuning of an efficient relaxation processes of the H-bond network and/or of the protein.     

Application of the Marcus theory for analysis of the temperature dependence of the reactions leading to photosynthetic water oxidation: results and implications

The temperature dependence of donor side reactions was analysed within the framework of the Marcus theory of nonadiabatic electron transfer. The following results were obtained for PS II membrane fragments from spinach: (1) the reorganisation energy of P680^+? reduction by Y_Z is of the order of 0.5?eV in samples with a functionally fully competent water oxidising complex (WOC); (2) destruction of the WOC by Tris-washing gives rise to a drastic increase of λ to values of the order of 1.6?eV; (3) the reorganisation energies of the oxidation steps in the WOC are dependent, on the redox states S _i with values of about 0.6?eV for the reactions Y_Z ^OX S ₀→Y_Z S ₁ and Y_Z ^OX S ₁→Y_Z S ₂, 1.6?eV for the reaction Y_Z ^OX S ₂→Y_Z S ₃ and 1.1?eV (above a characteristic temperature u_c of about 6??°C) for the reaction Y_Z ^OX S ₃→→Y_Z S ₀+O₂. Using an empirical rate constant-distance relationship, the van der Waals distance between Y_Z and P680 was found to be about 10?Å, independent of the presence or absence of the WOC, whereas the distance between Y_Z and the manganese cluster in the WOC was ≥15?Å. Based on the calculated activation energies the environment of Y_Z is inferred to be almost "dry" and hydrophobic when the WOC is intact but becomes enriched with water molecules after WOC destruction. Furthermore, it is concluded that the transition S ₂→S ₃ is an electron transfer reaction gated by a conformational change, i.e. it comprises significant structural changes of functional relevance. Measurements of kinetic H/D isotope exchange effects support the idea that none of these reactions is gated by the break of a covalent O-H bond. The implications of these findings for the mechanism of water oxidation are discussed.     

Free radicals generated during oxidation of green tea polyphenols: Electron paramagnetic resonance spectroscopy combined with density functional theory calculations

Electron paramagnetic resonance spectroscopy and density functional theory calculations have been used to investigate the redox properties of the green tea polyphenols (GTPs) (?)-epigallocatechin gallate (EGCG), (?)-epigallocatechin (EGC), and (?)-epicatechin gallate (ECG). Aqueous extracts of green tea and these individual phenols were autoxidized at alkaline pH and oxidized by superoxide anion (O₂^?) radicals in dimethyl sulfoxide. Several new aspects of the free radical chemistry of GTPs were revealed. EGCG can be oxidized on both the B and the D ring. The B ring was the main oxidation site during autoxidation, but the D ring was the preferred site for O₂^? oxidation. Oxidation of the D ring was followed by structural degradation, leading to generation of a radical identical to that of oxidized gallic acid. Alkaline autoxidation of green tea extracts produced four radicals that were related to products of the oxidation of EGCG, EGC, ECG, and gallic acid, whereas the spectra from O₂^? oxidation could be explained solely by radicals generated from EGCG. Assignments of hyperfine coupling constants were made by DFT calculations, allowing the identities of the radicals observed to be confirmed.     

Prevention of cardiolipin oxidation and fatty acid cycling as two antioxidant mechanisms of cationic derivatives of plastoquinone (SkQs)

The present state of the art in studies on the mechanisms of antioxidant activities of mitochondria-targeted cationic plastoquinone derivatives (SkQs) is reviewed. Our experiments showed that these compounds can operate as antioxidants in two quite different ways, i.e. (i) by preventing peroxidation of cardiolipin [Antonenko et al., Biochemistry (Moscow) 73 (2008) 1273–1287] and (ii) by fatty acid cycling resulting in mild uncoupling that inhibits the formation of reactive oxygen species (ROS) in mitochondrial State 4 [Severin et al. Proc. Natl. Acad. Sci. USA 107 (2009), 663–668]. The quinol and cationic moieties of SkQ are involved in cases (i) and (ii), respectively. In case (i) SkQH₂ interrupts propagation of chain reactions involved in peroxidation of unsaturated fatty acid residues in cardiolipin, the formed SkQ^? being reduced back to SkQH₂ by heme b_H of complex III in an antimycin-sensitive way. Molecular dynamics simulation showed that there are two stable conformations of SkQ1 with the quinol residue localized near peroxyl radicals at C₉ or C₁₃ of the linoleate residue in cardiolipin. In mechanism (ii), fatty acid cycling mediated by the cationic SkQ moiety is involved. It consists of (a) transmembrane movement of the fatty acid anion/SkQ cation pair and (b) back flows of free SkQ cation and protonated fatty acid. The cycling results in a protonophorous effect that was demonstrated in planar phospholipid membranes and liposomes. In mitochondria, the cycling gives rise to mild uncoupling, thereby decreasing membrane potential and ROS generation coupled to reverse electron transport in the respiratory chain. In yeast cells, dodecyltriphenylphosphonium (С₁₂TPP), the cationic part of SkQ1, induces uncoupling that is mitochondria-targeted since С₁₂TPP is specifically accumulated in mitochondria and increases the H⁺ conductance of their inner membrane. The conductance of the outer cell membrane is not affected by С₁₂TPP.     

Lipid Peroxide-Derived Short-Chain Carbonyls Mediate Hydrogen Peroxide-Induced and Salt-Induced Programmed Cell Death in Plants

Lipid peroxide-derived toxic carbonyl compounds (oxylipin carbonyls), produced downstream of reactive oxygen species (ROS), were recently revealed to mediate abiotic stress-induced damage of plants. Here, we investigated how oxylipin carbonyls cause cell death. When tobacco (Nicotiana tabacum) Bright Yellow-2 (BY-2) cells were exposed to hydrogen peroxide, several species of short-chain oxylipin carbonyls [i.e. 4-hydroxy-(E)-2-nonenal and acrolein] accumulated and the cells underwent programmed cell death (PCD), as judged based on DNA fragmentation, an increase in terminal deoxynucleotidyl transferase dUTP nick end labeling-positive nuclei, and cytoplasm retraction. These oxylipin carbonyls caused PCD in BY-2 cells and roots of tobacco and Arabidopsis (Arabidopsis thaliana). To test the possibility that oxylipin carbonyls mediate an oxidative signal to cause PCD, we performed pharmacological and genetic experiments. Carnosine and hydralazine, having distinct chemistry for scavenging carbonyls, significantly suppressed the increase in oxylipin carbonyls and blocked PCD in BY-2 cells and Arabidopsis roots, but they did not affect the levels of ROS and lipid peroxides. A transgenic tobacco line that overproduces 2-alkenal reductase, an Arabidopsis enzyme to detoxify α,β-unsaturated carbonyls, suffered less PCD in root epidermis after hydrogen peroxide or salt treatment than did the wild type, whereas the ROS level increases due to the stress treatments were not different between the lines. From these results, we conclude that oxylipin carbonyls are involved in the PCD process in oxidatively stressed cells. Our comparison of the ability of distinct carbonyls to induce PCD in BY-2 cells revealed that acrolein and 4-hydroxy-(E)-2-nonenal are the most potent carbonyls. The physiological relevance and possible mechanisms of the carbonyl-induced PCD are discussed.In plants, environmental stressors such as extreme temperatures, drought, intense UV-B radiation, and soil salinity can cause tissue damage, growth inhibition, and even death. These detrimental effects are often ascribed to the action of reactive oxygen species (ROS) produced in the stressed plants for the following reasons: (1) various environmental stressors commonly cause the oxidation of biomolecules in plants; and (2) transgenic plants with enhanced antioxidant capacities show improved tolerance to environmental stressors (Suzuki et al., 2014). The production of ROS such as superoxide anion radical and hydrogen peroxide (H₂O₂) is intrinsically associated with photosynthesis and respiration (Foyer and Noctor, 2003; Asada, 2006).Plant cells are equipped with abundant antioxidant molecules such as α-tocopherol, β-carotene, and ascorbic acid and an array of ROS-scavenging enzymes such as superoxide dismutase and ascorbate peroxidase to maintain low intracellular ROS levels. When plants are exposed to severe and prolonged environmental stress, the balance between the production and scavenging of ROS is disrupted and the cellular metabolism reaches a new state of higher ROS production and lower antioxidant capacity. Then, the oxidation of vital biomolecules such as proteins and DNA proceeds, and as a consequence, cells undergo oxidative injury (Mano, 2002). The cause-effect relationship between ROS and tissue injury in plants is thus widely accepted, but the biochemical processes between the generation of ROS and cell death are poorly understood.Increasing evidence shows that oxylipin carbonyls mediate the oxidative injury of plants (Yamauchi et al., 2012; for review, see Mano, 2012; Farmer and Mueller, 2013). Oxylipin carbonyls are a group of carbonyl compounds derived from oxygenated lipids and fatty acids. The production of oxylipin carbonyls in living cells is explained as follows. Lipids in the membranes are constitutively oxidized by ROS to form lipid peroxides (LOOHs; Mène-Saffrané et al., 2007) because they are the most immediate and abundant targets near the ROS production sites. There are two types of LOOH formation reaction from ROS (Halliwell and Gutteridge, 2007). One is the radical-dependent reaction. Highly oxidizing radicals, such as hydroxyl radical (standard reduction potential of the HO^•/H₂O pair, +2.31 V) and the protonated form of superoxide radical (HO₂/H₂O₂, +1.06 V), can abstract a hydrogen atom from a lipid molecule, especially at the central carbon of a pentadiene structure in a polyunsaturated fatty acid, to form a radical. This organic radical rapidly reacts with molecular oxygen, forming a lipid hydroperoxyl radical, which then abstracts a hydrogen atom from a neighboring molecule and becomes a LOOH. The other reaction is the addition of singlet oxygen to a double bond of an unsaturated fatty acid to form an endoperoxide or a hydroperoxide (both are LOOHs). A variety of LOOH species are formed, depending on the source fatty acid and also by the oxygenation mechanism (Montillet et al., 2004). LOOH molecules are unstable, and in the presence of redox catalysts such as transition metal ions or free radicals, they decompose to form various aldehydes and ketones (i.e. oxylipin carbonyls; Farmer and Mueller, 2013). The chemical species of oxylipin carbonyl formed in the cells differ according to the fatty acids and the type of ROS involved (Grosch, 1987; Mano et al., 2014a).More than a dozen species of oxylipin carbonyls are formed in plants (for review, see Mano et al., 2009). Oxylipin carbonyls are constitutively formed in plants under normal physiological conditions, and the levels of certain types of oxylipin carbonyls rise severalfold under stress conditions, detected as increases in the free carbonyl content (Mano et al., 2010; Yin et al., 2010; Kai et al., 2012) and by the extent of the carbonyl modification of target proteins (Winger et al., 2007; Mano et al., 2014b). Among the oxylipin carbonyls, the α,β-unsaturated carbonyls, such as acrolein and 4-hydroxy-(E)-2-nonenal (HNE), have high reactivity and cytotoxicity (Esterbauer et al., 1991; Alméras et al., 2003). They strongly inactivate lipoate enzymes in mitochondria (Taylor et al., 2002) and thiol-regulated enzymes in chloroplasts (Mano et al., 2009) in vitro and cause tissue injury in leaves when they are fumigated (Matsui et al., 2012).The physiological relevance of oxylipin carbonyls has been shown by the observation that the overexpression of different carbonyl-scavenging enzymes commonly confers stress tolerance to transgenic plants (for review, see Mano, 2012). For example, 2-alkenal reductase (AER)-overproducing tobacco (Nicotiana tabacum) showed tolerance to aluminum (Yin et al., 2010), aldehyde dehydrogenase-overproducing Arabidopsis (Arabidopsis thaliana) showed tolerance to osmotic and oxidative stress (Sunkar et al., 2003), and aldehyde reductase-overproducing tobacco showed tolerance to chemical and drought stress (Oberschall et al., 2000). In addition, the genetic suppression of a carbonyl-scavenging enzyme made plants susceptible to stressors (Kotchoni et al., 2006; Shin et al., 2009; Yamauchi et al., 2012; Tang et al., 2014). Under stress conditions, there are positive correlations between the levels of certain carbonyls and the extent of tissue injury (Mano et al., 2010; Yin et al., 2010; Yamauchi et al., 2012). Thus, it is evident that oxylipin carbonyls, downstream products of ROS, are causes of oxidative damage in plant cells.To investigate how oxylipin carbonyls damage cells in oxidatively stressed plants, we here examined the mode of cell death that is induced by oxylipin carbonyls and identified the carbonyl species responsible for the cell death. We observed that oxylipin carbonyls cause programmed cell death (PCD), and our results demonstrated that the oxylipin carbonyls mediate the oxidative stress-induced PCD in tobacco Bright Yellow-2 (BY-2) cultured cells and in roots of tobacco and Arabidopsis plants. We then estimated the relative strengths of distinct carbonyl species to initiate the PCD program. Our findings demonstrate a critical role of the lipid metabolites in ROS signaling.     

On the use of fluorescence lifetime imaging and dihydroethidium to detect superoxide in intact animals and ex vivo tissues: A reassessment

Recently, D.J. Hall et al. reported that ethidium (E⁺) is formed as a major product of hydroethidine (HE) or dihydroethidium reaction with superoxide (O₂⁻) in intact animals with low tissue oxygen levels (J. Cereb. Blood Flow Metab. 32:23–32, 2012). The authors concluded that measurement of E⁺ is an indicator of O₂⁻ formation in intact brains of animals. This finding is in stark contrast to previous reports using in vitro systems showing that 2-hydroxyethidium, not ethidium, is formed from the reaction between O₂⁻ and HE. Published in vivo results support the in vitro findings. In this study, we performed additional experiments in which HE oxidation products were monitored under different fluxes of O₂⁻. Results from these experiments further reaffirm our earlier findings (H. Zhao et al., Free Radic. Biol. Med. 34:1359, 2003). We conclude that whether in vitro or in vivo, E⁺ measured by HPLC or by fluorescence lifetime imaging is not a diagnostic marker product for O₂⁻ reaction with HE.