Simulations show that a small part of variable chlorophyll a fluorescence originates in photosystem I and contributes to overall fluorescence rise

From leaf to multiscale models of photosynthesis: applications and challenges for crop improvement

To keep up with the growth of human population and to circumvent deleterious effects of global climate change, it is essential to enhance crop yield to achieve higher production. Here we review mathematical models of oxygenic photosynthesis that are extensively used, and discuss in depth a subset that accounts for diverse approaches providing solutions to our objective. These include models (1) to study different ways to enhance photosynthesis, such as fine-tuning antenna size, photoprotection and electron transport; (2) to bioengineer carbon metabolism; and (3) to evaluate the interactions between the process of photosynthesis and the seasonal crop dynamics, or those that have included statistical whole-genome prediction methods to quantify the impact of photosynthesis traits on the improvement of crop yield. We conclude by emphasizing that the results obtained in these studies clearly demonstrate that mathematical modelling is a key tool to examine different approaches to improve photosynthesis for better productivity, while effective multiscale crop models, especially those that also include remote sensing data, are indispensable to verify different strategies to obtain maximized crop yields.

From remotely sensed solar-induced chlorophyll fluorescence to ecosystem structure, function, and service: Part I-Harnessing theory

Solar-induced chlorophyll fluorescence (SIF) is a remotely sensed optical signal emitted during the light reactions of photosynthesis. The past two decades have witnessed an explosion in availability of SIF data at increasingly higher spatial and temporal resolutions, sparking applications in diverse research sectors (e.g., ecology, agriculture, hydrology, climate, and socioeconomics). These applications must deal with complexities caused by tremendous variations in scale and the impacts of interacting and superimposing plant physiology and three-dimensional vegetation structure on the emission and scattering of SIF. At present, these complexities have not been overcome. To advance future research, the two companion reviews aim to (1) develop an analytical framework for inferring terrestrial vegetation structures and function that are tied to SIF emission, (2) synthesize progress and identify challenges in SIF research via the lens of multi-sector applications, and (3) map out actionable solutions to tackle these challenges and offer our vision for research priorities over the next 5-10 years based on the proposed analytical framework. This paper is the first of the two companion reviews, and theory oriented. It introduces a theoretically rigorous yet practically applicable analytical framework. Guided by this framework, we offer theoretical perspectives on three overarching questions: (1) The forward (mechanism) question-How are the dynamics of SIF affected by terrestrial ecosystem structure and function? (2) The inference question: What aspects of terrestrial ecosystem structure, function, and service can be reliably inferred from remotely sensed SIF and how? (3) The innovation question: What innovations are needed to realize the full potential of SIF remote sensing for real-world applications under climate change? The analytical framework elucidates that process complexity must be appreciated in inferring ecosystem structure and function from the observed SIF; this framework can serve as a diagnosis and inference tool for versatile applications across diverse spatial and temporal scales.

PCA-based detection of phosphorous deficiency in wheat plants using prompt fluorescence and 820 nm modulated reflection signals

Phosphorus deficiency induces biochemical and morphological changes which affect crop yield and production. Prompt fluorescence signal characterizes the PSII activity and electron transport from PSII to PSI, while the modulated light reflection at 820 (MR 820) nm investigates the redox state of photosystem I (PSI) and plastocyanin (PC). Therefore, combining information from modulated reflection at 820 nm with chlorophyll a fluorescence can potentially provide a more complete understanding of the photosynthetic process and integrating other plant physiological measurements may help to increase the accuracy of detecting the phosphorus deficiency in wheat leaves. In our study, we combined the chlorophyll a fluorescence and MR 820 signals to study the response of wheat plants to phosphorus deficiency as indirect tools for phosphorus plant status characterization. In addition, we studied the changes in chlorophyll content index, stomatal conductance (gs), root morphology, and biomass of wheat plants. The results showed an alteration in the electron transport chain as a specific response to P deficiency in the I-P phase during the reduction of the acceptor side of PSI. Furthermore, P deficiency increased parameters related to the energy fluxes per reaction centers, namely ETo/RC, REo/RC, ABS/RC, and DIo/RC. P deficiency increased the values of MRmin and MRmax and decreased νred, which implies that the reduction of PSI and PC became slower as the phosphorus decreased. The principal component analysis of the modulated reflection and chlorophyll a fluorescence parameters, with the integration of the growth parameters as supplementary variables, accounted for over 71% of the total variance in our phosphorus data using two components and provided a reliable information on PSII and PSI photochemistry under P deficiency.

An exploratory steady-state redox model of photosynthetic linear electron transport for use in complete modelling of photosynthesis for broad applications

A photochemical model of photosynthetic electron transport (PET) is needed to integrate photophysics, photochemistry, and biochemistry to determine redox conditions of electron carriers and enzymes for plant stress assessment and mechanistically link sun-induced chlorophyll fluorescence to carbon assimilation for remotely sensing photosynthesis. Towards this goal, we derived photochemical equations governing the states and redox reactions of complexes and electron carriers along the PET chain. These equations allow the redox conditions of the mobile plastoquinone pool and the cytochrome b₆ f complex (Cyt) to be inferred with typical fluorometry. The equations agreed well with fluorometry measurements from diverse C₃ /C₄ species across environments in the relationship between the PET rate and fraction of open photosystem II reaction centres. We found the oxidation of plastoquinol by Cyt is the bottleneck of PET, and genetically improving the oxidation of plastoquinol by Cyt may enhance the efficiency of PET and photosynthesis across species. Redox reactions and photochemical and biochemical interactions are highly redundant in their complex controls of PET. Although individual reaction rate constants cannot be resolved, they appear in parameter groups which can be collectively inferred with fluorometry measurements for broad applications. The new photochemical model developed enables advances in different fronts of photosynthesis research.

Light-induced changes of far-red excited chlorophyll fluorescence: further evidence for variable fluorescence of photosystem I in vivo

Recently, the long-standing paradigm of variable chlorophyll (Chl) fluorescence (Fv) in vivo originating exclusively from PSII was challenged, based on measurements with green algae and cyanobacteria (Schreiber and Klughammer 2021, PRES 149, 213-231). Fv(I) was identified by comparing light-induced changes of Fv > 700 nm and Fv < 710 nm. The Fv(I) induced by strong light was about 1.5 × larger in Fv > 700 nm compared to Fv < 710 nm. In the present communication, concentrating on the model green alga Chlorella vulgaris, this work is extended by comparing the light-induced changes of long-wavelength fluorescence (> 765 nm) that is excited by either far-red light (720 nm, mostly absorbed in PSI) or visible light (540 nm, absorbed by PSI and PSII). Polyphasic rise curves of Fv induced by saturating 540 nm light are measured, which after normalization of the initial O-I₁ rises, assumed to reflect Fv(II), display a 2 × higher I₂-P transient with 720 nm excitation (720ex) compared with 540ex. Analysis of the Fo(I) contributions to Fo(720ex) and Fo(540ex) reveals that also Fo(I)720ex is 2 × higher than Fo(I)540ex, which supports the notion that the whole I₂-P transient is due to Fv(I). The twofold increase of the excitation ratio of F(I)/F(II) from 680 to 720 nm is much smaller than the eight-tenfold increase of PSI/PSII known from action spectra. It is suggested that the measured F > 765 nm is not representative for the bulk chlorophyll of PSI, but rather reflects a small fraction of far-red absorbing chlorophyll forms ("red Chls") with particular properties. Based on the same approach (comparison of polyphasic rise curves measured with 720ex and 540ex), the existence of Fv(I) is confirmed in a variety of other photosynthetic organisms (cyanobacteria, moss, fern, higher plant leaves).

Determining photosynthetic control, a probe for the balance between electron transport and Calvin-Benson cycle activity, with the DUAL-KLAS-NIR

Photosynthetic Control is defined as the control imposed on photosynthetic electron transport by the lumen-pH-sensitive re-oxidation of plastoquinol (PQH₂) by cytochrome b₆f. Photosynthetic Control leads at higher actinic light intensities to an electron transport chain with a (relatively) reduced photosystem (PS) II and PQ pool and a (relatively) oxidized PS I. Making Light Curves of more than 33 plant species with the recently introduced DUAL-KLAS-NIR (Chl a fluorescence + the redox states of plastocyanin (PC), P700, and ferredoxin (Fd)) the light intensity-dependent induction of Photosynthetic Control was probed and characterized. It was observed that PC became completely oxidized at light intensities ≤ 400 µmol photons m^-2 s^-1 (at lower light intensities in shade than in sun leaves). The relationship between qP and P700(red) was used to determine the extent of Photosynthetic Control. Instead of measuring the whole Light Curve, it was shown that a single moderate light intensity can be used to characterize the status of a leaf relative to that of other leaves. It was further found that in some shade-acclimated leaves Fd becomes again more oxidized at high light intensities indicating that electron transfer from the PQ pool to P700 cannot keep up with the outflow of electrons on the acceptor side of PS I. It was observed as well that for NPQ-induction a lower light intensity (less acidified lumen) was needed than for the induction of Photosynthetic Control. The measurements were also used to make a comparison between the parameters qP and qL, a comparison suggesting that qP was the more relevant parameter.

Molecular, Brownian, kinetic and stochastic models of the processes in photosynthetic membrane of green plants and microalgae

The paper presents the results of recent work at the Department of Biophysics of the Biological Faculty, Lomonosov Moscow State University on the kinetic and multiparticle modeling of processes in the photosynthetic membrane. The detailed kinetic models and the rule-based kinetic Monte Carlo models allow to reproduce the fluorescence induction curves and redox transformations of the photoactive pigment P700 in the time range from 100 ns to dozens of seconds and make it possible to reveal the role of individual carriers in their formation for different types of photosynthetic organisms under different illumination regimes, in the presence of inhibitors, under stress conditions. The fitting of the model curves to the experimental data quantifies the reaction rate constants that cannot be directly measured experimentally, including the non-radiative thermal relaxation reactions. We use the direct multiparticle models to explicitly describe the interactions of mobile photosynthetic carrier proteins with multienzyme complexes both in solution and in the biomembrane interior. An analysis of these models reveals the role of diffusion and electrostatic factors in the regulation of electron transport, the influence of ionic strength and pH of the cellular environment on the rate of electron transport reactions between carrier proteins. To describe the conformational intramolecular processes of formation of the final complex, in which the actual electron transfer occurs, we use the methods of molecular dynamics. The results obtained using kinetic and molecular models supplement our knowledge of the mechanisms of organization of the photosynthetic electron transport processes at the cellular and molecular levels.

Photosynthesis dynamics and regulation sensed in the frequency domain

Foundations of photosynthesis research have been established mainly by studying the response of plants to changing light, typically to sudden exposure to a constant light intensity after dark acclimation or light flashes. This approach remains valid and powerful, but can be limited by requiring dark acclimation before time-domain measurements and often assumes that rate constants determining the photosynthetic response do not change between dark and light acclimation. We show that these limits can be overcome by measuring plant responses to sinusoidally modulated light of varying frequency. By its nature, such frequency-domain characterization is performed in light-acclimated plants with no need for prior dark acclimation. Amplitudes, phase shifts, and upper harmonic modulation extracted from the data for a wide range of frequencies can target different kinetic domains and regulatory feedbacks. The occurrence of upper harmonic modulation reflects nonlinear phenomena, including photosynthetic regulation. To support these claims, we measured chlorophyll fluorescence emission of the green alga Chlorella sorokiniana in light that was sinusoidally modulated in the frequency range 1000-0.001 Hz. Based on these experimental data and numerical as well as analytical mathematical models, we propose that frequency-domain measurements can become a versatile tool in plant sensing.

Evidence for variable chlorophyll fluorescence of photosystem I in vivo

Room temperature fluorescence in vivo and its light-induced changes are dominated by chlorophyll a fluorescence excited in photosystem II, F(II), peaking around 685 nm. Photosystem I fluorescence, F(I), peaking around 730 nm, so far has been assumed to be constant in vivo. Here, we present evidence for significant contributions of F(I) to variable fluorescence in the green unicellular alga Chlorella vulgaris, the cyanobacterium Synechococcus leopoliensis and a light-green ivy leaf. A Multi-Color-PAM fluorometer was applied for measurements of the polyphasic fluorescence rise (O-I1-I2-P) induced by strong 440 nm light in a dilute suspension of Chlorella, with detection alternating between emission above 700 nm (F > 700) and below 710 nm (F < 710). By averaging 10 curves each of the F > 700 and F < 710 recordings even small differences could be reliably evaluated. After equalizing the amplitudes of the O-I1 phase, which constitutes a specific F(II) response, the O-I1-I2 parts of the two recordings were close to identical, whereas the I2-P phase was larger in F > 700 than in F < 710 by a factor of 1.42. In analogous measurements with Synechococcus carried out in the dark state 2 using strong 625 nm actinic light, after O-I1 equalization the I2-P phase in F > 700 exceeded that in F < 710 even by a factor of 1.99. In measurements with Chlorella, the I2-P phase and with it the apparent variable fluorescence of PS I, Fv(I), were suppressed by moderate actinic background light and by the plastoquinone antagonist DBMIB. Analogous measurements with leaves are rendered problematic by unavoidable light intensity gradients and the resulting heterogenic origins of F > 700 and F < 710. However, a light-green young ivy leaf gave qualitatively similar results as those obtained with the suspensions, thus strongly suggesting the existence of Fv(I) also in leaves.

Simultaneously measuring pulse-amplitude-modulated (PAM) chlorophyll fluorescence of leaves at wavelengths shorter and longer than 700 nm

PAM fluorescence of leaves of cherry laurel (Prunus laurocerasus L.) was measured simultaneously in the spectral range below 700 nm (sw) and above 700 nm (lw). A high-sensitivity photodiode was employed to measure the low intensities of sw fluorescence. Photosystem II (PSII) performance was analyzed by the saturation pulse method during a light response curve with subsequent dark phase. The sw fluorescence was more variable, resulting in higher PSII photochemical yields compared to lw fluorescence. The variations between sw and lw data were explained by different levels of photosystem I (PSI) fluorescence: the contribution of PSI fluorescence to minimum fluorescence (F₀) was calculated to be 14% at sw wavelengths and 45% at lw wavelengths. With the results obtained, the validity of an earlier method for the quantification of PSI fluorescence (Genty et al. in Photosynth Res 26:133-139, 1990, https://doi.org/10.1007/BF00047085 ) was reconsidered. After subtracting PSI fluorescence from all fluorescence levels, the maximum PSII photochemical yield (F_V/F_M) in the sw range was 0.862 and it was 0.883 in the lw range. The lower F_V/F_M at sw wavelengths was suggested to arise from inactive PSII reaction centers in the outermost leaf layers. Polyphasic fluorescence transients (OJIP or OI₁I₂P kinetics) were recorded simultaneously at sw and lw wavelengths: the slowest phase of the kinetics (IP or I₂P) corresponded to 11% and 13% of total variable sw and lw fluorescence, respectively. The idea that this difference is due to variable PSI fluorescence is critically discussed. Potential future applications of simultaneously recording fluorescence in two spectral windows include studies of PSI non-photochemical quenching and state I-state II transitions, as well as measuring the fluorescence from pH-sensitive dyes simultaneously with chlorophyll fluorescence.

Photosynthesis: basics, history and modelling

BACKGROUND

With limited agricultural land and increasing human population, it is essential to enhance overall photosynthesis and thus productivity. Oxygenic photosynthesis begins with light absorption, followed by excitation energy transfer to the reaction centres, primary photochemistry, electron and proton transport, NADPH and ATP synthesis, and then CO2 fixation (Calvin-Benson cycle, as well as Hatch-Slack cycle). Here we cover some of the discoveries related to this process, such as the existence of two light reactions and two photosystems connected by an electron transport 'chain' (the Z-scheme), chemiosmotic hypothesis for ATP synthesis, water oxidation clock for oxygen evolution, steps for carbon fixation, and finally the diverse mechanisms of regulatory processes, such as 'state transitions' and 'non-photochemical quenching' of the excited state of chlorophyll a.

SCOPE

In this review, we emphasize that mathematical modelling is a highly valuable tool in understanding and making predictions regarding photosynthesis. Different mathematical models have been used to examine current theories on diverse photosynthetic processes; these have been validated through simulation(s) of available experimental data, such as chlorophyll a fluorescence induction, measured with fluorometers using continuous (or modulated) exciting light, and absorbance changes at 820 nm (ΔA820) related to redox changes in P700, the reaction centre of photosystem I.

CONCLUSIONS

We highlight here the important role of modelling in deciphering and untangling complex photosynthesis processes taking place simultaneously, as well as in predicting possible ways to obtain higher biomass and productivity in plants, algae and cyanobacteria.

Maximum fluorescence and electron transport kinetics determined by light-induced fluorescence transients (LIFT) for photosynthesis phenotyping

Photosynthetic phenotyping requires quick characterization of dynamic traits when measuring large plant numbers in a fluctuating environment. Here, we evaluated the light-induced fluorescence transient (LIFT) method for its capacity to yield rapidly fluorometric parameters from 0.6 m distance. The close approximation of LIFT to conventional chlorophyll fluorescence (ChlF) parameters is shown under controlled conditions in spinach leaves and isolated thylakoids when electron transport was impaired by anoxic conditions or chemical inhibitors. The ChlF rise from minimum fluorescence (Fo) to maximum fluorescence induced by fast repetition rate (Fm-FRR) flashes was dominated by reduction of the primary electron acceptor in photosystem II (QA). The subsequent reoxidation of QA- was quantified using the relaxation of ChlF in 0.65 ms (Fr1) and 120 ms (Fr2) phases. Reoxidation efficiency of QA- (Fr1/Fv, where Fv = Fm-FRR - Fo) decreased when electron transport was impaired, while quantum efficiency of photosystem II (Fv/Fm) showed often no significant effect. ChlF relaxations of the LIFT were similar to an independent other method. Under increasing light intensities, Fr2'/Fq' (where Fr2' and Fq' represent Fr2 and Fv in the light-adapted state, respectively) was hardly affected, whereas the operating efficiency of photosystem II (Fq'/Fm') decreased due to non-photochemical quenching. Fm-FRR was significantly lower than the ChlF maximum induced by multiple turnover (Fm-MT) flashes. However, the resulting Fv/Fm and Fq'/Fm' from both flashes were highly correlated. The LIFT method complements Fv/Fm with information about efficiency of electron transport. Measurements in situ and from a distance facilitate application in high-throughput and automated phenotyping.

Maximum fluorescence and electron transport kinetics determined by light-induced fluorescence transients (LIFT) for photosynthesis phenotyping

Photosynthetic phenotyping requires quick characterization of dynamic traits when measuring large plant numbers in a fluctuating environment. Here, we evaluated the light-induced fluorescence transient (LIFT) method for its capacity to yield rapidly fluorometric parameters from 0.6 m distance. The close approximation of LIFT to conventional chlorophyll fluorescence (ChlF) parameters is shown under controlled conditions in spinach leaves and isolated thylakoids when electron transport was impaired by anoxic conditions or chemical inhibitors. The ChlF rise from minimum fluorescence (F_o) to maximum fluorescence induced by fast repetition rate (F_m-FRR) flashes was dominated by reduction of the primary electron acceptor in photosystem II (Q_A). The subsequent reoxidation of Q_A^- was quantified using the relaxation of ChlF in 0.65 ms (F_r1) and 120 ms (F_r2) phases. Reoxidation efficiency of Q_A^- (F_r1/F_v, where F_v = F_m-FRR - F_o) decreased when electron transport was impaired, while quantum efficiency of photosystem II (F_v/F_m) showed often no significant effect. ChlF relaxations of the LIFT were similar to an independent other method. Under increasing light intensities, F_r2'/F_q' (where F_r2' and F_q' represent F_r2 and F_v in the light-adapted state, respectively) was hardly affected, whereas the operating efficiency of photosystem II (F_q'/F_m') decreased due to non-photochemical quenching. F_m-FRR was significantly lower than the ChlF maximum induced by multiple turnover (F_m-MT) flashes. However, the resulting F_v/F_m and F_q'/F_m' from both flashes were highly correlated. The LIFT method complements F_v/F_m with information about efficiency of electron transport. Measurements in situ and from a distance facilitate application in high-throughput and automated phenotyping.

Exogenous application of cytokinin during dark senescence eliminates the acceleration of photosystem II impairment caused by chlorophyll b deficiency in barley

Recent studies have shown that chlorophyll (Chl) b has an important role in the regulation of leaf senescence. However, there is only limited information about senescence of plants lacking Chl b and senescence-induced decrease in photosystem II (PSII) and photosystem I (PSI) function has not even been investigated in such plants. We have studied senescence-induced changes in photosynthetic pigment content and PSII and PSI activities in detached leaves of Chl b-deficient barley mutant, chlorina f2^f2 (clo). After 4 days in the dark, the senescence-induced decrease in PSI activity was smaller in clo compared to WT leaves. On the contrary, the senescence-induced impairment in PSII function (estimated from Chl fluorescence parameters) was much more pronounced in clo leaves, even though the relative decrease in Chl content was similar to wild type (WT) leaves (Hordeum vulgare L., cv. Bonus). The stronger impairment of PSII function seems to be related to more pronounced damage of reaction centers of PSII. Interestingly, exogenously applied plant hormone cytokinin 6-benzylaminopurine (BA) was able to maintain PSII function in the dark senescing clo leaves to a similar extent as in WT. Thus, considering the fact that without BA the senescence-induced decrease in PSII photochemistry in clo was more pronounced than in WT, the relative protective effect of BA was higher in Chl b-deficient mutant than in WT.

Simulation of chlorophyll fluorescence rise and decay kinetics, and P700-related absorbance changes by using a rule-based kinetic Monte-Carlo method

A model of primary photosynthetic reactions in the thylakoid membrane was developed and its validity was tested by simulating three types of experimental kinetic curves: (1) the light-induced chlorophyll a fluorescence rise (OJIP transients) reflecting the stepwise transition of the photosynthetic electron transport chain from the oxidized to the fully reduced state; (2) the dark relaxation of the flash-induced fluorescence yield attributed to the Q_A^- oxidation kinetics in PSII; and (3) the light-induced absorbance changes near 820 or 705 nm assigned to the redox transitions of P₇₀₀ in PSI. A model was implemented by using a rule-based kinetic Monte-Carlo method and verified by simulating experimental curves under different treatments including photosynthetic inhibitors, heat stress, anaerobic conditions, and very high light intensity.

Kinetics of photosystem II electron transport: a mathematical analysis based on chlorophyll fluorescence induction

The OJDIP rise in chlorophyll fluorescence during induction at different light intensities was mathematically modeled using 24 master equations describing electron transport through photosystem II (PSII) plus ordinary differential equations for electron budgets in plastoquinone, cytochrome f, plastocyanin, photosystem I, and ferredoxin. A novel feature of the model is consideration of electron in- and outflow budgets resulting in changes in redox states of Tyrosine Z, P680, and Q_A as sole bases for changes in fluorescence yield during the transient. Ad hoc contributions by transmembrane electric fields, protein conformational changes, or other putative quenching species were unnecessary to account for primary features of the phenomenon, except a peculiar slowdown of intra-PSII electron transport during induction at low light intensities. The lower than F _m post-flash fluorescence yield F _f was related to oxidized tyrosine Z. The transient J peak was associated with equal rates of electron arrival to and departure from Q_A and requires that electron transfer from Q_A^- to Q_B be slower than that from Q_A^- to Q_B^-. Strong quenching by oxidized P680 caused the dip D. Reduced plastoquinone, a competitive product inhibitor of PSII, blocked electron transport proportionally with its concentration. Electron transport rate indicated by fluorescence quenching was faster than the rate indicated by O₂ evolution, because oxidized donor side carriers quench fluorescence but do not transport electrons. The thermal phase of the fluorescence rise beyond the J phase was caused by a progressive increase in the fraction of PSII with reduced Q_A and reduced donor side.

Frequently asked questions about chlorophyll fluorescence, the sequel

Using chlorophyll (Chl) a fluorescence many aspects of the photosynthetic apparatus can be studied, both in vitro and, noninvasively, in vivo. Complementary techniques can help to interpret changes in the Chl a fluorescence kinetics. Kalaji et al. (Photosynth Res 122:121-158, 2014a) addressed several questions about instruments, methods and applications based on Chl a fluorescence. Here, additional Chl a fluorescence-related topics are discussed again in a question and answer format. Examples are the effect of connectivity on photochemical quenching, the correction of F V /F M values for PSI fluorescence, the energy partitioning concept, the interpretation of the complementary area, probing the donor side of PSII, the assignment of bands of 77 K fluorescence emission spectra to fluorescence emitters, the relationship between prompt and delayed fluorescence, potential problems when sampling tree canopies, the use of fluorescence parameters in QTL studies, the use of Chl a fluorescence in biosensor applications and the application of neural network approaches for the analysis of fluorescence measurements. The answers draw on knowledge from different Chl a fluorescence analysis domains, yielding in several cases new insights.

Modeling the light-induced electric potential difference ΔΨ across the thylakoid membrane based on the transition state rate theory

In photosynthesis, electron transport-coupled proton movement initiates the formation of the light-induced electric potential difference, ΔΨ, across the thylakoid membrane (TM). Ions are transported across the TM to counterbalance the charge of protons accumulated in the lumen. The objective of this work is to construct range of mathematical models for simulation of ΔΨ, using the transition state rate theory (TSRT) for description of movement of ions through the channels. The TSRT considers either single-ion (TSRT-SI) or multi-ion occupancy (TSRT-MI) in the channels. Movement of ions through the channel pore is described by means of energy barriers and binding sites; ions move in and out of vacant sites with rate constants that depend on the barrier heights and well depths, as well as on the interionic repulsion in TSRT-MI model. Three energy motifs are used to describe the TSRT-SI model: two-barrier one-site (2B1S), three-barrier two-site (3B2S), and four-barrier three-site (4B3S). The 3B2S energy motif is used for the TSRT-MI model. The accumulation of cations due to the TM surface negative fixed charges is also taken into account. A model employing the electro-diffusion theory instead of the TSRT is constructed for comparison. The dual wavelength transmittance signal (ΔA515-560nm) measuring the electrochromic shift (ECS) provides a proxy for experimental light-induced ΔΨ. The simulated ΔΨ traces qualitatively agree with the measured ECS traces. The models can simulate different channel conducting regimes and assess their impact on ΔΨ. The ionic flux coupling in the TSRT-MI model suggests that an increase in the internal or external K⁺ concentration may block the outward or the inward Mg²⁺ current, respectively.

Thylakoid membrane model of the Chl a fluorescence transient and P700 induction kinetics in plant leaves

A new Thylakoid model is presented, which describes in detail the electron/proton transfer reactions between membrane protein complexes including photosystems II and I (PSII, PSI), cytochrome (Cyt) b 6 f, mobile plastoquinone PQ pool in the thylakoid membrane, plastocyanin in lumen and ferredoxin in stroma, reduction of NADP via FNR and cyclic electron transfer. The Thylakoid model parameters were fitted both to Chl fluorescence induction data (FI) and oxido-reductions of P700 (ΔA 810) measured from 20 μs up to 20 s in pea leaves. The two-wave kinetics of FI and ΔA 810 (O(JI)PSM and OABCDE) were described quantitatively, provided that the values of membrane electrochemical potential components ΔΨ(t), pHL(t)/pHS(t) are in physiologically relevant ranges. The time courses on the time scale from nanoseconds to tens of seconds of oxido-reduction changes of ET components as well as concentrations of proton/ions (K+, Cl-) were calculated. We assume a low constant FNR activity over this period. Charge movements across the thylakoid membrane by passive leakage and active ATPase transport and proton buffer reactions are simulated. The dynamics of charge fluxes during photosynthetic induction under low light (PFD 200 μmol photons m-2 s-1) were analyzed. The initial wave of P700 oxidation within 20 ms during independent operation of PSI and PSII was followed after 50 ms by PSI donor-side reduction from reduced PQ pool via Cyt b 6 f site. The Cyt b 6 f reactions contribute to the stabilization of fluxes in the time range 1 s < t < 10 s. The detailed analysis of Chl a fluorescence at the PSM stage (t > 10 s) would need the investigation of FNR activation effect in order to explain the transitions between cyclic and linear electron transport.

The slow phase of chlorophyll a fluorescence induction in silico: Origin of the S-M fluorescence rise

In higher plants, algae, and cyanobacteria, chlorophyll (Chl) a fluorescence induction (ChlFI) has a fast (under a second) increasing OJIP phase and a slow (few minutes) PS(M)T phase, where O is for origin, the minimum fluorescence, J and I for intermediate levels, P for peak, S for a semi-steady state, M for a maximum (which is sometimes missing), and T for the terminal steady-state level. We have used a photosynthesis model of Ebenhöh et al. (Philos Trans R Soc B, 2014, doi: 10.1098/rstb.2013.0223 ) in an attempt to simulate the slow PS(M)T phase and to determine the origin of the S-M rise in Chlamydomonas (C.) reinhardtii cells. Our experiments in silico show that a slow fluorescence S-M rise (as that observed, e.g., by Kodru et al. (Photosynth Res 125:219-231, 2015) can be simulated only if the photosynthetic samples are initially in a so-called "state 2," when the absorption cross section (CS) of Photosystem II (PSII) is lower than that of PSI, and Chl a fluorescence is low (see, e.g., a review by Papageorgiou and Govindjee (J Photochem Photobiol B 104:258-270, 2011). In this case, simulations show that illumination induces a state 2 (s2) to state 1 (s1) transition (qT₂₁), and a slow S-M rise in the simulated ChlFI curve, since the fluorescence yield is known to be higher in s1, when CS of PSII is larger than that of PSI. Additionally, we have analyzed how light intensity and several photosynthetic processes influence the degree of this qT₂₁, and thus the relative amplitude of the simulated S-M phase. A refinement of the photosynthesis model is, however, necessary in order to obtain a better fit of the simulation data with the measured ChlFI curves.

Obstacles in the quantification of the cyclic electron flux around Photosystem I in leaves of C3 plants

Sixty years ago Arnon and co-workers discovered photophosphorylation driven by a cyclic electron flux (CEF) around Photosystem I. Since then understanding the physiological roles and the regulation of CEF has progressed, mainly via genetic approaches. One basic problem remains, however: quantifying CEF in the absence of a net product. Quantification of CEF under physiological conditions is a crucial prerequisite for investigating the physiological roles of CEF. Here we summarize current progress in methods of CEF quantification in leaves and, in some cases, in isolated thylakoids, of C3 plants. Evidently, all present methods have their own shortcomings. We conclude that to quantify CEF in vivo, the best way currently is to measure the electron flux through PS I (ETR1) and that through PS II and PS I in series (ETR2) for the whole leaf tissue under identical conditions. The difference between ETR1 and ETR2 is an upper estimate of CEF, mainly consisting, in C3 plants, of a major PGR5-PGRL1-dependent CEF component and a minor chloroplast NDH-dependent component, where PGR5 stands for Proton Gradient Regulation 5 protein, PGRL1 for PGR5-like photosynthesis phenotype 1, and NDH for Chloroplast NADH dehydrogenase-like complex. These two CEF components can be separated by the use of antimycin A to inhibit the former (major) component. Membrane inlet mass spectrometry utilizing stable oxygen isotopes provides a reliable estimation of ETR2, whilst ETR1 can be estimated from a method based on the photochemical yield of PS I, Y(I). However, some issues for the recommended method remain unresolved.

Reduced minimum model for the photosynthetic induction processes in photosystem I

Photosystem I (PS I) is one of the most important protein complexes for photosynthesis, which is present in plants, algae and cyanobacteria. A variety of mechanisms for environmental response in and around PS I have been elucidated experimentally and theoretically. During the photosynthetic induction time, the congestion of electron occurs in PS I and then the over-reduced PS I states are realized. This means that the degree of freedom of the redox states of PS I becomes large and thus the understanding of phenomena based on the model describing PS I in the state space becomes difficult. To understand the phenomena intuitively, we have reduced the complicated PS I model which has the multi-timescale property for electron and excitation-energy transfer processes into a simple one which has only the mono-timescale property through the use of hierarchical coarse-graining (HCG) method. The coarse-grained model describes the state of PS I by seven variable states, while the original model describes the PS I by 3×2(7)(=384) states. Based on the derived model, the I820 (820nm transmittance signal) curve in photosynthetic induction term, which indicates the accumulations of P700(+) and Pc(+), is simulated and analyzed in comparison with experiment. With respect to this signal curve, it is revealed that the initial increase up to the shoulder at 10(-3) s, the increase from that point to the peak at 2 ×10(-2) s, and the decay after that peak reflect the accumulations of P700(+), Pc(+) and P700FA(-)FB(-) (PS I state in which P700,FA(-) and FB(-) are observed.), respectively. Besides, the important role of the charge recombination processes from P700(+)A0A(-) and P700(+)A1A(-) states for the dissipation of the extra absorbed energy in photosynthetic induction period is confirmed.

Systems approach to excitation-energy and electron transfer reaction networks in photosystem II complex: model studies for chlorophyll a fluorescence induction kinetics

Photosystem II (PS II) is a protein complex which evolves oxygen and drives charge separation for photosynthesis employing electron and excitation-energy transfer processes over a wide timescale range from picoseconds to milliseconds. While the fluorescence emitted by the antenna pigments of this complex is known as an important indicator of the activity of photosynthesis, its interpretation was difficult because of the complexity of PS II. In this study, an extensive kinetic model which describes the complex and multi-timescale characteristics of PS II is analyzed through the use of the hierarchical coarse-graining method proposed in the authors׳ earlier work. In this coarse-grained analysis, the reaction center (RC) is described by two states, open and closed RCs, both of which consist of oxidized and neutral special pairs being in quasi-equilibrium states. Besides, the PS II model at millisecond scale with three-state RC, which was studied previously, could be derived by suitably adjusting the kinetic parameters of electron transfer between tyrosine and RC. Our novel coarse-grained model of PS II can appropriately explain the light-intensity dependent change of the characteristic patterns of fluorescence induction kinetics from O-J-I-P, which shows two inflection points, J and I, between initial point O and peak point P, to O-J-D-I-P, which shows a dip D between J and I inflection points.

Modeling of the redox state dynamics in photosystem II of Chlorella pyrenoidosa Chick cells and leaves of spinach and Arabidopsis thaliana from single flash-induced fluorescence quantum yield changes on the 100 ns-10 s time scale

The time courses of the photosystem II (PSII) redox states were analyzed with a model scheme supposing a fraction of 11-25 % semiquinone (with reduced [Formula: see text]) RCs in the dark. Patterns of single flash-induced transient fluorescence yield (SFITFY) measured for leaves (spinach and Arabidopsis (A.) thaliana) and the thermophilic alga Chlorella (C.) pyrenoidosa Chick (Steffen et al. Biochemistry 44:3123-3132, 2005; Belyaeva et al. Photosynth Res 98:105-119, 2008, Plant Physiol Biochem 77:49-59, 2014) were fitted with the PSII model. The simulations show that at high-light conditions the flash generated triplet carotenoid (3)Car(t) population is the main NPQ regulator decaying in the time interval of 6-8 μs. So the SFITFY increase up to the maximum level [Formula: see text]/F 0 (at ~50 μs) depends mainly on the flash energy. Transient electron redistributions on the RC redox cofactors were displayed to explain the SFITFY measured by weak light pulses during the PSII relaxation by electron transfer (ET) steps and coupled proton transfer on both the donor and the acceptor side of the PSII. The contribution of non-radiative charge recombination was taken into account. Analytical expressions for the laser flash, the (3)Car(t) decay and the work of the water-oxidizing complex (WOC) were used to improve the modeled P680(+) reduction by YZ in the state S 1 of the WOC. All parameter values were compared between spinach, A. thaliana leaves and C. pyrenoidosa alga cells and at different laser flash energies. ET from [Formula: see text] slower in alga as compared to leaf samples was elucidated by the dynamics of [Formula: see text] fractions to fit SFITFY data. Low membrane energization after the 10 ns single turnover flash was modeled: the ∆Ψ(t) amplitude (20 mV) is found to be about 5-fold smaller than under the continuous light induction; the time-independent lumen pHL, stroma pHS are fitted close to dark estimates. Depending on the flash energy used at 1.4, 4, 100 % the pHS in stroma is fitted to 7.3, 7.4, and 7.7, respectively. The biggest ∆pH difference between stroma and lumen was found to be 1.2, thus pH- dependent NPQ was not considered.

Assessment of the impact of photosystem I chlorophyll fluorescence on the pulse-amplitude modulated quenching analysis in leaves of Arabidopsis thaliana

In their natural environment, plants are exposed to varying light conditions, which can lead to a build-up of excitation energy in photosystem (PS) II. Non-photochemical quenching (NPQ) is the primary defence mechanism employed to dissipate this excess energy. Recently, we developed a fluorescence-quenching analysis procedure that enables the protective effectiveness of NPQ in intact Arabidopsis leaves to be determined. However, pulse-amplitude modulation measurements do not currently allow distinguishing between PSII and PSI fluorescence levels. Failure to account for PSI contribution is suggested to lead to inaccurate measurements of NPQ and, particularly, maximum PSII yield (F v/F m). Recently, Pfündel et al. (Photosynth Res 114:189-206, 2013) proposed a method that takes into account PSI contribution in the measurements of F o fluorescence level. However, when PSI contribution was assumed to be constant throughout the induction of NPQ, we observed lower values of the measured minimum fluorescence level ([Formula: see text]) than those calculated according to the formula of Oxborough and Baker (Photosynth Res 54:135-142 1997) ([Formula: see text]), regardless of the light intensity. Therefore, in this work, we propose a refined model to correct for the presence of PSI fluorescence, which takes into account the previously observed NPQ in PSI. This method efficiently resolves the discrepancies between measured and calculated F o' produced by assuming a constant PSI fluorescence contribution, whilst allowing for the correction of the maximum PSII yield.

Parameters of photosynthetic energy partitioning

Almost every laboratory dealing with plant physiology, photosynthesis research, remote sensing, and plant phenotyping possesses a fluorometer to measure a kind of chlorophyll (Chl) fluorescence induction (FLI). When the slow Chl FLI is measured with addition of saturating pulses and far-red illumination, the so-called quenching analysis followed by the so-called relaxation analysis in darkness can be realized. These measurements then serve for evaluation of the so-called energy partitioning, that is, calculation of quantum yields of photochemical and of different types of non-photochemical processes. Several theories have been suggested for photosynthetic energy partitioning. The current work aims to summarize all the existing theories, namely their equations for the quantum yields, their meaning and their assumptions. In the framework of these theories it is also found here that the well-known NPQ parameter ( [Formula: see text] ; Bilger and Björkman, 1990) equals the ratio of the quantum yield of regulatory light-induced non-photochemical quenching to the quantum yield of constitutive non-regulatory non-photochemical quenching (ΦNPQ/Φf,D). A similar relationship is also found here for the PQ parameter (ΦP/Φf,D).

Modeling chlorophyll a fluorescence transient: relation to photosynthesis

To honor Academician Alexander Abramovitch Krasnovsky, we present here an educational review on the relation of chlorophyll a fluorescence transient to various processes in photosynthesis. The initial event in oxygenic photosynthesis is light absorption by chlorophylls (Chls), carotenoids, and, in some cases, phycobilins; these pigments form the antenna. Most of the energy is transferred to reaction centers where it is used for charge separation. The small part of energy that is not used in photochemistry is dissipated as heat or re-emitted as fluorescence. When a photosynthetic sample is transferred from dark to light, Chl a fluorescence (ChlF) intensity shows characteristic changes in time called fluorescence transient, the OJIPSMT transient, where O (the origin) is for the first measured minimum fluorescence level; J and I for intermediate inflections; P for peak; S for semi-steady state level; M for maximum; and T for terminal steady state level. This transient is a real signature of photosynthesis, since diverse events can be related to it, such as: changes in redox states of components of the linear electron transport flow, involvement of alternative electron routes, the build-up of a transmembrane pH gradient and membrane potential, activation of different nonphotochemical quenching processes, activation of the Calvin-Benson cycle, and other processes. In this review, we present our views on how different segments of the OJIPSMT transient are influenced by various photosynthetic processes, and discuss a number of studies involving mathematical modeling and simulation of the ChlF transient. A special emphasis is given to the slower PSMT phase, for which many studies have been recently published, but they are less known than on the faster OJIP phase.

Fluorescence F 0 of photosystems II and I in developing C3 and C 4 leaves, and implications on regulation of excitation balance

This work addresses the question of occurrence and function of photosystem II (PSII) in bundle sheath (BS) cells of leaves possessing NADP-malic enzyme-type C4 photosynthesis (Zea mays). Although no requirement for PSII activity in the BS has been established, several component proteins of PSII have been detected in BS cells of developing maize leaves exhibiting O2-insensitive photosynthesis. We used the basal fluorescence emissions of PSI (F 0I) and PSII (F 0II) as quantitative indicators of the respective relative photosystem densities. Chl fluorescence induction was measured simultaneously at 680 and 750 nm. In mature leaves, the F m(680)/F 0(680) ratio was 10.5 but less in immature leaves. We propose that the lower ratio was caused by the presence of a distinct non-variable component, F c, emitting at 680 and 750 nm. After F c was subtracted, the fluorescence of PSI (F 0I) was detected as a non-variable component at 750 nm and was undetectably low at 680 nm. Contents of Chls a and b were measured in addition to Chl fluorescence. The Chl b/(a + b) was relatively stable in developing sunflower leaves (0.25-0.26), but in maize it increased from 0.09 to 0.21 with leaf tissue age. In sunflower, the F 0I/(F 0I + F 0II) was 0.39 ± 0.01 independent of leaf age, but in maize, this parameter was 0.65 in young tissue of very low Chl content (20-50 mg m(-2)) falling to a stable level of 0.53 ± 0.01 at Chl contents >100 mg m(-2). The values of F 0I/(F 0I + F 0II) showed that in sunflower, excitation was partitioned between PSII and PSI in a ratio of 2:1, but the same ratio was 1:1 in the C4 plant. The latter is consistent with a PSII:PSI ratio of 2:1 in maize mesophyll cells and PSI only in BS cells (2:1:1 distribution). We suggest, moreover, that redox mediation of Chl synthesis, rather than protein accumulation, regulates photosystem assembly to ensure optimum excitation balance between functional PSII and PSI. Indeed, the apparent necessity for two Chls (a and b) may reside in their targeted functions in influencing accumulation of PSI and PSII, respectively, as opposed to their spectral differences.

Computer modeling of electron and proton transport in chloroplasts

Photosynthesis is one of the most important biological processes in biosphere, which provides production of organic substances from atmospheric CO2 and water at expense of solar energy. In this review, we contemplate computer models of oxygenic photosynthesis in the context of feedback regulation of photosynthetic electron transport in chloroplasts, the energy-transducing organelles of the plant cell. We start with a brief overview of electron and proton transport processes in chloroplasts coupled to ATP synthesis and consider basic regulatory mechanisms of oxygenic photosynthesis. General approaches to computer simulation of photosynthetic processes are considered, including the random walk models of plastoquinone diffusion in thylakoid membranes and deterministic approach to modeling electron transport in chloroplasts based on the mass action law. Then we focus on a kinetic model of oxygenic photosynthesis that includes key stages of the linear electron transport, alternative pathways of electron transfer around photosystem I (PSI), transmembrane proton transport and ATP synthesis in chloroplasts. This model includes different regulatory processes: pH-dependent control of the intersystem electron transport, down-regulation of photosystem II (PSII) activity (non-photochemical quenching), the light-induced activation of the Bassham-Benson-Calvin (BBC) cycle. The model correctly describes pH-dependent feedback control of electron transport in chloroplasts and adequately reproduces a variety of experimental data on induction events observed under different experimental conditions in intact chloroplasts (variations of CO2 and O2 concentrations in atmosphere), including a complex kinetics of P700 (primary electron donor in PSI) photooxidation, CO2 consumption in the BBC cycle, and photorespiration. Finally, we describe diffusion-controlled photosynthetic processes in chloroplasts within the framework of the model that takes into account complex architecture of chloroplasts and lateral heterogeneity of lamellar system of thylakoids. The lateral profiles of pH in the thylakoid lumen and in the narrow gap between grana thylakoids have been calculated under different metabolic conditions. Analyzing topological aspects of diffusion-controlled stages of electron and proton transport in chloroplasts, we conclude that along with the NPQ mechanism of attenuation of PSII activity and deceleration of PQH2 oxidation by the cytochrome b6f complex caused by the lumen acidification, the intersystem electron transport may be down-regulated due to the light-induced alkalization of the narrow partition between adjacent thylakoids of grana. The computer models of electron and proton transport described in this article may be integrated as appropriate modules into a comprehensive model of oxygenic photosynthesis.

Model based analysis of transient fluorescence yield induced by actinic laser flashes in spinach leaves and cells of green alga Chlorella pyrenoidosa Chick

Measurements of Single Flash Induced Transient Fluorescence Yield (SFITFY) on spinach leaves and whole cells of green thermophilic alga Chlorella pyrenoidosa Chick were analyzed for electron transfer (ET) steps and coupled proton transfer (PT) on both the donor and the acceptor side of the reaction center (RC) of photosystem II (PS II). A specially developed PS II model (Belyaeva et al., 2008, 2011a) allowed the determination of ET steps that occur in a hierarchically ordered time scale from nanoseconds to several seconds. Our study demonstrates that our SFITFY data is consistent with the concept of the reduction of P680(+) by YZ in both leaves and algae (studied on spinach leaves and cells of Chlorella pyrenoidosa Chick). The multiphasic P680(+) reduction kinetics by YZ in PS II core complexes with high oxygen evolution capacity was seen in both algae and leaves. Model simulation to fit SFITFY curves for dark adapted species used here gives the rate constants to verify nanosecond kinetic stages of P680(+) reduction by YZ in the redox state S1 of the water oxidizing complex (WOC) shown in Kühn et al. (2004). Then a sequence of relaxation steps in the redox state S1, outlined by Renger (2012), occurs in both algae and leaves as a similar non-adiabatic ET reactions. Coupled PT is discussed briefly to understand a rearrangement of hydrogen bond protons in the protein matrix of the WOC (Umena et al., 2011). On the other hand, present studies showed a slower reoxidation of reduced QA by QB in algal cells as compared with that in a leaf that might be regarded as a consequence of differences of spatial domains at the QB-site in leaves compared to algae. Our comparative study helped to correlate theory with experimental data for molecular photosynthetic mechanisms in thylakoid membranes.

Photosynthetic proton and electron transport in wheat leaves under prolonged moderate drought stress

In conditions of long-lasting moderate drought stress, we have studied the photoprotective responses in leaves of wheat (Triticum aestivum L., cv. Katya) related to the photosynthetic electron and proton transport. The dark-interval relaxation kinetics of electrochromic bandshift (ECS) indicated a decrease of electric and an increase of osmotic component of the proton motive force in drought stressed leaves, but neither the total proton motive force (pmf) nor the thylakoid proton conductance (gH(+)) were affected. We observed the enhanced protection against overreduction of PSI acceptor side in leaves of drought stressed plants. This was obviously achieved by the rapid buildup of transthylakoid pH gradient at relatively low light intensities, directly associated to the steep increase of NPQ and the down-regulation of linear electron transport. It was further accompanied by the steep increase of redox poise at PSII acceptor side and PSI donor side. The early responses related to thylakoid lumen acidification in drought-stressed leaves could be associated with the activity of an enhanced fraction of PSI not involved in linear electron flow, which may have led to enhanced cyclic electron pathway even in relatively low light intensities, as well as to the drought-induced decrease of IP-amplitude in fast chlorophyll fluorescence kinetics.