Flash-induced oxygen evolution in photosynthesis: simple solution for the extended S-state model that includes misses, double-hits, inactivation, and backward-transitions

Flash-induced oxygen evolution in higher plants, algae, and cyanobacteria exhibits damped period-four oscillations. To explain such oscillations, Kok suggested a simple phenomenological S-state model, in which damping is due to empirical misses and double-hits. Here we developed an analytical solution for the extended Kok model that includes misses, double-hits, inactivation, and backward-transitions. The solution of the classic Kok model (with misses and double-hits only) can be obtained as a particular case of this solution. Simple equations describing the flash-number dependence of individual S-states and oxygen evolution in both cases are almost identical and, therefore, the classic Kok model does not have a significant advantage in its simplicity over the extended version considered in this article. Developed equations significantly simplify the fitting of experimental data via standard nonlinear regression analysis and make unnecessary the use of many previously developed methods for finding parameters of the model. The extended Kok model considered here can provide additional insight into the effect of dark relaxation between flashes and inactivation.     

The Kok Effect in Chlamydomonas reinhardi

A Haxo-Blinks rate-measuring oxygen electrode together with a modulated light source gave an average current signal (change in net O₂ exchange) and a modulated current signal (photosynthetic O₂ evolution). Using this apparatus, net O₂ exchange and photosynthetic O₂ evolution at low intensities have been studied in the green alga, Chlamydomonas reinhardi. At both 645 nm and 695 nm, the curves of net O₂ exchange as a function of light intensity were steeper at lowest intensities than about compensation, indicative of the Kok effect. The effect was greater at 695 nm than at 645 nm. The corresponding curves of photosynthetic O₂ evolution, on the other hand, showed no Kok effect; here, the slope was lowest at lowest intensity. The absence of the Kok effect in O₂ evolution, together with its sensitivity to monofluoroacetic acid, show that it is due to an interaction of photosynthesis and respiration. The effect was exaggerated by 3-(3,4-dichlorophenyl)-1,1-dimethylurea. In the presence of concentrations of this inhibitor sufficient to inhibit O₂ evolution completely, a light-induced change in net O₂ exchange remained. This was interpreted as a system I dependent depression of respiratory O₂ uptake. The Kok effect remained undiminished in concentrations of carbonyl cyanide m-chlorophenylhydrazone and 2,4-dinitrophenol which partially uncoupled either oxidative phosphorylation alone or both oxidative and photosynthetic phosphorylations. The above results can be explained within a model of the Kok effect in which O₂ uptake is depressed by diversion of reductant away from respiratory electron transport and into photosystem I. The same photodepression of O₂ uptake also appears to account for a transient in net O₂ exchange seen in several algae upon turning off the light.     

Period-four oscillations of the flash-induced oxygen formation in photosynthesis*

In this minireview, the earlier researches that led to the discovery of the period-four oscillations of the flash-induced oxygen formation are presented. It also includes the background of the classical model proposed by Bessel Kok, in which the formation of oxygen requires the sequential accumulation of four positive charges on the donor side of the same reaction center. This revised version was published online in August 2006 with corrections to the Cover Date.     

The influence of anions on oxygen evolution by isolated spinach chloroplasts

A study has been made of the onset of chloride deprivation on the oxygen-evolving characteristics of isolated spinach chloroplasts. Using a modulated oxygen electrode it is found that the type of inhibition depends on the anion replacing chloride in the bathing medium. With nitrate a large increase in phase lag accompanies a relatively small inhibition which can be shown to be consistent with a decrease in the rate constant of the reaction which limits the rate of electron transport between water and Photosystem II. With sulphate there is a very small phase change but a larger inhibition which suggests that replacing chloride with sulphate in an electron-transport chain shuts off that chain. With acetate there is a moderate increase in phase lag and the largest inhibitory effect. The phase-lag increase suggests that acetate is affecting the same chloride-sensitive site as nitrate. However, the inhibition cannot be explained by this effect alone and points to the existence of a second chloride-sensitive site. Of the four forward reactions associated with the Kok model of oxygen evolution (Kok, B., Forbush, B. and McGloin, M. (1970) Photochem. Photobiol. 11, 457–475) only S1₃ → S₀ is slowed down when chloride is replaced by nitrate. This reaction is not slowed down by replacing chloride with sulphate.     

The interaction of nitrite with photosynthetic electron transport under anaerobic conditions

Chlorella cells were examined in a modulated oxygen polarograph under aerobic and anaerobic conditions. At light intensities below about 600 ergs · cm^?2 · s^?1 of 650 nm light, the oxygen yield and phase lag are lower under anaerobic conditions. Addition of 25 mM sodium nitrite increases both these parameters to values close to those found in the presence of oxygen. It is proposed that nitrite is reduced by Photosystem I thus diverting electrons from the cyclic electron transport pathway. The intersystem electron transport chain becomes more oxidized and this suppresses a backflow of electrons to the oxidizing side of Photosystem II, hence increasing the oxygen yield and the phase lag. The removal of oxygen from the bathing medium also alters the response of dark adapted _Chlorella to a series of saturating light flashes. In terms of the Kok model of Photosystem II (Kok, B., Forbush, B. and McGloin, M. (1970) Photochem. Photobiol. 11, 457–475) there is a large increase in the parameter α. Addition of nitrite reverses this change and virtually restores the response seen in the presence of oxygen. The deactivation of the S₂ state is greatly speeded up in the absence of oxygen but the addition of nitrite again reverses this.     

A trajectory of increasing activity and the elaboration of chemosensory modality: a new perspective on vertebrate origins

This article reviews recent advances in comparative biological studies of vertebrate origins, with the aim of revisiting the long-standing controversy concerning these origins. Since early vertebrate evolution is paralleled by an evolutionary trend towards increasing activity, I focus on the evolution of respiratory and circulatory systems and discuss their potential roles in early vertebrate evolution. I give particular attention to the nasohypophyseal duct, an orifice characteristically found in agnathan vertebrates, and hypothesize that this duct originally functioned to convey oxygen dissolved in seawater to the respiratory gills. The chemosensory cell population that originated from the wall of the duct became the incipient olfactory organ and played a role in the organization of feeding behavior. An increase in chemosensory receptor genes via large-scale genomic evolution in the vertebrate lineage caused the repertoire of chemosensory cells to diversify and led to the appearance of the integrative center, including telencephalic structures typically lacking in protochordates.     

EPR/ENDOR characterization of the physical and electronic structure of the OEC Mn cluster

Electron paramagnetic resonance (EPR) spectroscopy has often played a crucial role in characterizing the various cofactors and processes of photosynthesis, and photosystem II and its oxygen evolving chemistry is no exception. Until recently, the application of EPR spectroscopy to the characterization of the oxygen evolving complex (OEC) has been limited to the S2-state of the Kok cycle. However, in the past few years, continuous wave-EPR signals have been obtained for both the S0- and S1-state as well as for the S2 (radical)(Z)-state of a number of inhibited systems. Furthermore, the pulsed EPR technique of electron spin echo electron nuclear double resonance spectroscopy has been used to directly probe the 55Mn nuclei of the manganese cluster. In this review, we discuss how the EPR data obtained from each of these states of the OEC Kok cycle are being used to provide insight into the physical and electronic structure of the manganese cluster and its interaction with the key tyrosine, Y(Z).     

Context-Dependent Evolutionary Models for Non-Coding Sequences: An Overview of Several Decades of Research and an Analysis of Laurasiatheria and Primate Evolution

The past decade has seen a growing interest in evolutionary models that relax the assumption of site-independent evolution for non-coding sequences. While phylogenetic inference using such so-called context-dependent models is currently computationally prohibitive, these models have been shown to yield significant increases in model fit compared to site-independent evolutionary models, which remain the most widely used evolutionary models to study substitution patterns and perform phylogenetic inference. Context-dependent models have been shown to be suited to study the spontaneous deamination of cytosine in mammalian sequences. In this paper, I discuss various approaches presented in recent years to model context-dependent evolution. I start with discussing the empirical research and results that have led to the development of these models. To accurately estimate the context-dependent substitution patterns that arise from these models, accurate sampling of substitution histories under such models is required. Further, appropriate model selection techniques to assess model performance has become more important than ever, given the drastic increase in parameters of context-dependent models and the tendency of older model selection techniques to prefer parameter-rich models. I also present new results on two mammalian datasets (Primate and Laurasiatheria data) to shed a light on so-called lineage-dependent context-dependent evolution. I conclude this paper with a discussion on current challenges in the development of context-dependent modeling approaches.     

Flash kinetics and light intensity dependence of oxygen evolution in the blue-green alga Anacystis nidulans

Patterns of oxygen evolution in flashing light for the blue-green alga Anacystis nidulans are compared with those for broken spinach chloroplasts and whole cells of the green alga Chlorella pyrenoidosa. The oscillations of oxygen yield with flash number that occur in both Anacystis and Chlorella, display a greater degree of damping than do those of isolated spinach chloroplasts. The increase in damping results from a two- to threefold increase in the fraction (α) of reaction centers “missed” by a flash. The increase in α cannot be explained by non-saturating flash intensities or by the dark reduction of the oxidized intermediates formed by the flash. Anaerobic conditions markedly increase α in Anacystis and Chlorella but have no effect on α in broken spinach chloroplasts. The results signify that the mechanism of charge separation and water oxidation involved in all three organisms is the same, but that the pool of secondary electron acceptors between Photosystem II and Photosystem I is more reduced in the dark, in the algal cells, than in the isolated spinach chloroplasts.Oxygen evolution in flashing light for Anacystis and Chlorella show light saturation curves for the oxygen yield of the third flash (Y₃) that differ markedly from those of the steady-state flashes (Y_s). In experiments in which all flashes are uniformly attenuated, Y₃ requires nearly twice as much light as Y_s to reach half-saturation. Under these conditions Y₃ has a sigmoidal dependence on intensity, while that of Y_s is hyperbolic. These differences depend on the number of flashes attenuated. When any one of the first three flashes is attenuated, the variation of Y₃ with intensity resembles that of Y_s. When two of the first three flashes are attenuated, Y₃ is intermediate in shape between the two extremes. A quantitative interpretation of these results based on the model of Kok et al. (Kok, B., Forbush, B. and McGloin, M. (1970) Photochem. Photobiol. 11, 457–475, and Forbush, B., Kok, B. and McGloin, M. P. (1971) Photochem. Photobiol. 14, 307–321) fits the experimental data.     

How fast can Photosystem II split water? Kinetic performance at high and low frequencies

Molecular oxygen evolution from water is a universal signature of oxygenic photosynthesis. Detection of the presence, speed and efficiency of the enzymatic machinery that catalyzes this process in vivo has been limited. We describe a laser-based fast repetition rate fluorometer (FRRF) that allows highly accurate and rapid measurements of these properties via the kinetics of Chl-a variable fluorescence yield (Fv) in living cells and leaves at repetition rates up to 10 kHz. Application to the detection of quenching of Fv is described and compared to flash-induced O₂ yield data. Period-four oscillations in both Fv and O₂, caused by stimulation of primary charge recombination by the O₂ evolving complex (WOC) within Photosystem II (PS II), are directly compared. The first quantitative calculations of the enzymatic parameters of the Kok model (α – miss; β – double hit; S-state populations) are reported from Fv data over a 5 kHz range of flash frequencies that is 100-fold wider than previously examined. Comparison of a few examples of cyanobacteria, green algae and spinach reveals that Arthrospira m., a cyanobacterium that thrives in alkaline carbonate lakes, exhibits the fastest water-splitting rates ever observed thus farin vivo. In all oxygenic phototrophs examined thus far, an unprecedented large increase in the Kok α and β parameters occur at both high and low flash frequencies, which together with their strong correlation, indicates that PS II-WOC centers split water at remarkably lower efficiencies and possibly by different mechanisms at these extreme flash frequencies. Revisions to the classic Kok model are anticipated.     

Apparatus and mechanism of photosynthetic oxygen evolution: a personal perspective*

This historical minireview describes basic lines of progress in our understanding of the functional pattern of photosynthetic water oxidation and the structure of the Photosystem II core complex. After a short introduction into the state of the art about 35 years ago, results are reviewed that led to identification of the essential cofactors of this process and the kinetics of their reactions. Special emphasis is paid on the flash induced oxygen measurements performed by Pierre Joliot (in Paris, France) and Bessel Kok (Baltimore, MD) and their coworkers that led to the scheme, known as the Kok-cycle. These findings not only unraveled the reaction pattern of oxidation steps leading from water to molecular oxygen but also provided the essential fingerprint as prerequisite for studying individual redox reactions. Starting with the S. Singer and G. Nicolson model of membrane organization, attempts were made to gain information on the structure of the Photsystem II complex that eventually led to the current stage of knowledge based on the recently published X-ray crystal structure of 3.8 A resolution in Berlin (Germany).With respect to the mechanism of water oxidation, the impact of Gerald T. Babcock's hydrogen abstractor model and all the considerations of electron/proton transfer coupling are outlined. According to my own model cosiderations, the protein matrix is not only a 'cofactor holder' but actively participates by fine tuning via hydrogen bond networks, playing most likely an essential role in water substrate coordination and in oxygen-oxygen bond formation as the key step of the overall process.     

An investigation of water splitting in the Kok scheme of photosynthetic oxygen evolution

The involvement of OH bond breaking in the 4 dark reactions of the Kok scheme of photosynthetic oxygen evolution was investigated using Chlorella and spinach chloroplasts. When the photosynthetic material was suspended in a ²H₂O based medium, the reaction rates in all 4 cases were only slightly reduced as compared to the rates observed in an H₂O based medium. This was evidence that these rate processes were probably not limited by the breaking of an OH bond. Observations were also made on the yields of O₂ from dark adapted Chlorella subjected to a sequence of brief saturating light flashes. The oscillating flash yield sequence observed with algae suspended in ²H₂O showed greater damping of the oscillations than when the algae were suspended in H₂O. A computer fit of the Kok model to these results revealed a slightly higher proportion of misses, (i.e. absorbed quanta that do not drive photochemistry) in the ²H₂O case.     

Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins

Perspectives on the role of large‐effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular‐based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular‐based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome‐wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology.     

Characteristics of iodide activation and inhibition of oxygen evolution by photosystem II

Oxygen evolution by photosystem II (PSII) is activated by chloride and other monovalent anions. In this study, the effects of iodide on oxygen evolution activity were investigated using PSII-enriched membrane fragments from spinach. In the absence of Cl(-), the dependence of oxygen evolution activity on I(-) concentration showed activation followed by inhibition in both intact PSII and NaCl-washed PSII, which lacked the PsbP and PsbQ subunits. Using a substrate inhibition model, the range of values of the Michaelis constant K(M) in intact PSII (0.5-1.5 mM) was smaller than that in NaCl-washed PSII (1.5-5 mM), whereas values of the inhibition constant K(I) in intact PSII (9-17 mM) were larger than those in NaCl-washed PSII (1-4 mM). Studies of I(-) inhibition of Cl(-)-activated oxygen evolution in intact PSII revealed that I(-) was primarily an uncompetitive inhibitor, with uncompetitive constant K(i)' = 37 mM and Cl(-)-competitive constant K(i) > 200 mM. This result indicated that the activating Cl(-) must be bound for inhibition to take place, which is consistent with the substrate inhibition model for I(-) activation. The S(2) state multiline and g = 4.1 EPR signals in NaCl-washed PSII were examined in the presence of 3 and 25 mM NaI, corresponding to I(-)-activated and I(-)-inhibited conditions, respectively. The two S(2) state signals were observed at both I(-) concentrations, indicating that I(-) substitutes for Cl(-) in formation of the signals and that advancement to the S(2) state was not prevented by high I(-) concentrations. A model is presented that incorporates the results of this study, including the action of both chloride and iodide.     

Thermodynamically accurate modeling of the catalytic cycle of photosynthetic oxygen evolution: A mathematical solution to asymmetric Markov chains

Forty-three years ago, Kok and coworkers introduced a phenomenological model describing period-four oscillations in O₂ flash yields during photosynthetic water oxidation (WOC), which had been first reported by Joliot and coworkers. The original two-parameter Kok model was subsequently extended in its level of complexity to better simulate diverse data sets, including intact cells and isolated PSII-WOCs, but at the expense of introducing physically unrealistic assumptions necessary to enable numerical solutions. To date, analytical solutions have been found only for symmetric Kok models (inefficiencies are equally probable for all intermediates, called “S-states”). However, it is widely accepted that S-state reaction steps are not identical and some are not reversible (by thermodynamic restraints) thereby causing asymmetric cycles. We have developed a mathematically more rigorous foundation that eliminates unphysical assumptions known to be in conflict with experiments and adopts a new experimental constraint on solutions. This new algorithm termed STEAMM for S-state Transition Eigenvalues of Asymmetric Markov Models enables solutions to models having fewer adjustable parameters and uses automated fitting to experimental data sets, yielding higher accuracy and precision than the classic Kok or extended Kok models. This new tool provides a general mathematical framework for analyzing damped oscillations arising from any cycle period using any appropriate Markov model, regardless of symmetry. We illustrate applications of STEAMM that better describe the intrinsic inefficiencies for photon-to-charge conversion within PSII-WOCs that are responsible for damped period-four and period-two oscillations of flash O₂ yields across diverse species, while using simpler Markov models free from unrealistic assumptions.     

Enhancement studies on algae and isolated chloroplasts. Part II. Enhancement of oxygen evolution in intact chloroplasts.

Intact isolated chloroplasts were shown to exhibit a characteristic three-phase pattern of development of oxygen evolution activity. The first phase, Phase I, appeared to be an equilibration phase in which the isolated chloroplasts adapted to the conditions on the electrode surface. It was characterised by a rapidly increasing rate of oxygen evolution accompanied by decreasing enhancement signals. The second phase, Phase II, was an intermediate phase in which the rate of oxygen evolution was maximal and no enhancement was observed. In the last phase, Phase III, the rate of oxygen fell again, normal enhancement was still missing, but the samples appeared to undergo slow adaptive changes closely related to the State I-State II changes previously reported for whole cell systems. The concentrations of Mg2+ within the chloroplast were shown to play an important role in the control of the development of both the oxygen evolution and enhancement signals. It was shown how these signals could be explained in terms of a model that was consistent with that developed in Part I of this investigation to account for the variability of enhancement of the alga Chlorella pyrenoidosa.     

Spawning behaviour and acoustic communication in Atlantic cod

Cannibalism of small numbers of offspring by a parent has been proposed as an adaptive parental strategy, by providing energy to support parental care. There are few empirical studies, however, to support this hypothesis. The beaugregory damselfish, Stegastes leucostictus , is a marine teleost that does not actively ventilate its eggs by fanning them. Partial cannibalism is common in this species, but in field studies was found to be unrelated to ration level. Filial cannibalism differed from predation in the pattern of egg eating; filial cannibalism was characterised by a random pattern of egg loss from a clutch rather than an aggregated distribution. Embryos developed quicker and had higher survival rates when they were at low densities and in nest sites where oxygen levels were high, and experimental reduction of oxygen levels increased rates of filial cannibalism. Here I present a hypothesis for filial cannibalism in the beaugregory damselfish; males cannibalise egg clutches in order to reduce clutch density and improve oxygen supply to the remaining embryos. I use a model of filial cannibalism to demonstrate how oxygen mediated cannibalism may be adaptive, and discuss the evolution of filial cannibalism in the beaugregory damselfish and other teleosts.