Photosynthesis Research (v.125, #1-2)

In honor of Vladimir A. Shuvalov: light energy conversion in photosynthesis by Robert Carpentier; Suleyman I. Allakhverdiev (1-3).

My journey in photosynthesis research by Vladimir A. Shuvalov (5-8).
At the invitation of Suleyman I. Allakhverdiev, I provide here a brief autobiography for this special issue that recognizes my service and research for the larger international community of photosynthesis research.
Keywords: Primary photochemistry; (Bacterio)chlorophyll; (Bacterio)pheophytin; Reaction center of photosynthesis

Electron-vibrational relaxation in the excited state of the primary electron donor, bacteriochlorophyll dimer P, in the reaction centers (RCs) of purple photosynthetic bacteria Rhodobacter sphaeroides is modeled. A multimode model of three states (i.e., the ground state Pg, initially excited P1*, and relaxed excited P2*) is used to calculate the incoherent dynamics of the difference (ΔA) spectra on a femtosecond timescale for the YM210 W mutant RCs. The relaxation processes are described by the step-ladder model. The model shows that the electron-vibrational relaxation in the excited state of P is visualized by the transient red shift of the stimulated emission from P*. The dynamics of this shift is observed as a change in the ΔA spectrum shape in its red-most part, within a few hundreds of femtoseconds after excitation. As a result, an initial rise in the red-side ΔA kinetics is delayed with respect to the blue-side kinetics. The time constant of the P1* → P2* electronic relaxation (54 fs) and the Pg, P1*, and P2* vibrational relaxations (120 fs), used in the model, provided the best fit of the experimental time-resolved ΔA spectra and kinetics at 90 and 293 K. The possible nature of the P1* → P2* electronic relaxation is discussed.
Keywords: Photosynthesis; Charge separation; Reaction center; Electron transfer; Electron-vibrational relaxation

The L(M196)H mutation in Rhodobacter sphaeroides reaction center results in new electrostatic interactions by Tatiana Y. Fufina; Lyudmila G. Vasilieva; Azat G. Gabdulkhakov; Vladimir A. Shuvalov (23-29).
New histidine residue was introduced in M196 position in the reaction center of Rhodobacter sphaeroides in order to alter polarity of the BChl dimer’s protein environment and to study how it affects properties and structure of the primary electron donor P. It was shown that in the absorption spectrum of the mutant RC the 6 nm red shift of the Q Y P band was observed together with considerable decrease of its amplitude. The mid-point potential of P/P + in the mutant RC was increased by +65 (±15) mV as compared to the E m P/P + value in the wild-type RC suggesting that the mutation resulted in new pigment–protein interactions. Crystal structure of RC L(M196)H determined at 2.4 Å resolution implies that BChl Р В and introduced histidine-M196 organize new electrostatic contact that may be specified either as π–π staking or as hydrogen–π interaction. Besides, the structure of the mutants RC shows that His-M196 apparently became involved in hydrogen bond network existing in BChl Р В vicinity that may favor stability of the mutant RC.
Keywords: Photosynthetic reaction center; Bacteriochlorophyll; Site-directed mutagenesis; Rhodobacter sphaeroides ; Pigment–protein interactions; Electrostatic interactions

Orientation of B798 BChl a Q y transition dipoles in Chloroflexus aurantiacus chlorosomes: polarized transient absorption spectroscopy studies by Andrei Yakovlev; Vladimir Novoderezhkin; Alexandra Taisova; Vladimir Shuvalov; Zoya Fetisova (31-42).
Isotropic and anisotropic pump-probe spectra of Cfx. aurantiacus chlorosomes were measured on the fs-through ps-time scales for the B798 BChl a Q y band upon direct excitation of the B798 band at T = 293 K and T = 90 K. Upon direct excitation of the B798 band, the anisotropy parameter value r(λ) was constant within the whole BChl a Q y band at any delay time at both temperatures. The value of the anisotropy parameter r decayed from r = 0.4 at both temperatures (at 200 fs delay time after excitation) to the steady-state values r = 0.1 at T = 293 K and to r = 0.09 at T = 90 K (at 30 ÷ 100 ps delay time after excitation). The results were considered within the framework of the model of uniaxial orientation distribution of BChl-a transition dipoles within a single Cfx. aurantiacus chlorosome. This implies that the B798 BChl a Q y transition dipoles, randomly distributed around the normal to the baseplate plane, form the angle θ with the plane. For this model, the theoretical dependence of the steady-state anisotropy parameter r on the angle θ was derived. According to the theoretical dependence r(θ), the angle θ corresponding to the experimental steady-state value r = 0.1 at T = 293 K was found to equal 55°. As the temperature drops to 90 K, the angle θ decreases to 54°.
Keywords: Bacterial photosynthesis; Green bacteria; Chlorosome; Bacteriochlorophyll a antenna; Polarized pump-probe spectroscopy; Room and low-temperature spectroscopy

Low-temperature (77 K) phosphorescence of triplet chlorophyll in isolated reaction centers of photosystem II by Konstantin V. Neverov; Alexander A. Krasnovsky Jr; Alexey A. Zabelin; Vladimir A. Shuvalov; Anatoly Ya. Shkuropatov (43-49).
Phosphorescence characterized by the main emission band at 952 ± 1 nm (1.30 eV), the lifetime of 1.5 ± 0.1 ms and the quantum yield nearly equal to that for monomeric chlorophyll a in aqueous detergent dispersions, has been detected in isolated reaction centers (RCs) of spinach photosystem II at 77 K. The excitation spectrum shows maxima corresponding to absorption bands of chlorophyll a, pheophytin a, and β-carotene. The phosphorescence intensity strongly depends upon the redox state of RCs. The data suggest that the phosphorescence signal originates from the chlorophyll triplet state populated via charge recombination in the radical pair $${ m P}_{680}^{+}{ m Pheo}_{{ m D}1}^{-}.$$ P 680 + Pheo D 1 - .
Keywords: Photosystem II; Reaction center; Triplet state; Phosphorescence

Primary electron transfer processes in photosynthetic reaction centers from oxygenic organisms by Mahir Mamedov; Govindjee; Victor Nadtochenko; Alexey Semenov (51-63).
This minireview is written in honor of Vladimir A. Shuvalov, a pioneer in the area of primary photochemistry of both oxygenic and anoxygenic photosyntheses (See a News Report: Allakhverdiev et al. 2014). In the present paper, we describe the current state of the formation of the primary and secondary ion–radical pairs within photosystems (PS) II and I in oxygenic organisms. Spectral-kinetic studies of primary events in PS II and PS I, upon excitation by ~20 fs laser pulses, are now available and reviewed here; for PS II, excitation was centered at 710 nm, and for PS I, it was at 720 nm. In PS I, conditions were chosen to maximally increase the relative contribution of the direct excitation of the reaction center (RC) in order to separate the kinetics of the primary steps of charge separation in the RC from that of the excitation energy transfer in the antenna. Our results suggest that the sequence of the primary electron transfer reactions is P680 → ChlD1 → PheD1 → QA (PS II) and P700 → A 0A/A 0B → A 1A/A 1B (PS I). However, alternate routes of charge separation in PS II, under different excitation conditions, are not ruled out.
Keywords: Charge separation; Electron transfer; Photosystem II; Photosystem I; Primary processes; Pump-probe laser spectroscopy; Femtosecond time resolution

Regulation of photosynthetic electron transport at different levels of structural and functional organization of photosynthetic apparatus provides efficient performance of oxygenic photosynthesis in plants. This review begins with a brief overview of the chloroplast electron transport chain. Then two noninvasive biophysical methods (measurements of slow induction of chlorophyll a fluorescence and EPR signals of oxidized P700 centers) are exemplified to illustrate the possibility of monitoring induction events in chloroplasts in vivo and in situ. Induction events in chloroplasts are considered and briefly discussed in the context of short-term mechanisms of the following regulatory processes: (i) pH-dependent control of the intersystem electron transport; (ii) the light-induced activation of the Calvin–Benson cycle; (iii) optimization of electron transport due to fitting alternative pathways of electron flow and partitioning light energy between photosystems I and II; and (iv) the light-induced remodeling of photosynthetic apparatus and thylakoid membranes.
Keywords: Photosynthesis; Chloroplasts; Induction events; Regulation of photosynthetic electron transport

Effects of pH, Ca2+, and Cl ions on the extraction of Mn cations from oxygen-evolving complex (OEC) in Ca-depleted photosystem II (PSII(-Ca)) by exogenous reductants hydroquinone (H2Q) and H2O2 were studied. Two of 4 Mn cations are released by H2Q and H2O2 at pHs 5.7, 6.5, and 7.5, and their extraction does not depend on the presence of Ca2+ and Cl ions. One of Mn cations (“resistant” Mn cation) cannot be extracted by H2Q and H2O2 at any pH. Extraction of 4th Mn ion (“flexible” Mn cation) is sensitive to pH, Ca2+, and Cl. This Mn cation is released by reductants at pH 6.5 but not at pHs 5.7 and 7.5. A pH dependence curve of the oxygen-evolving activity in PSII(-Ca) membranes (in the presence of exogenous Ca2+) has a bell-shaped form with the maximum at pH 6.5. Thus, the increase in the resistance of flexible Mn cation in OEC to the action of reductants at acidic and alkaline pHs coincides with the decrease in oxygen evolution activity at these pHs. Exogenous Ca2+ protects the extraction of flexible Mn cation at pH 6.5. High concentration of Cl anions (100 mM) shifts the pH optimum of oxygen evolution to alkaline region (around pH 7.5), while the pH of flexible Mn extraction is also shifted to alkaline pH. This result suggests that flexible Mn cation plays a key role in the water-splitting reaction. The obtained results also demonstrate that only one Mn cation in Mn4 cluster is under strong control of calcium. The change in the flexible Mn cation resistance to exogenous reductants in the presence of Ca2+ suggests that Ca2+ can control the redox potential of this cation.
Keywords: Photosystem II; Oxygen-evolving complex; Manganese; Hydroquinone; Hydrogen peroxide; Calcium; Chloride

Acaryochloris marina is a unique cyanobacterium that contains chlorophyll (Chl) d as a major pigment. Because Chl d has smaller excitation energy than Chl a used in ordinary photosynthetic organisms, the energetics of the photosystems of A. marina have been the subject of interest. It was previously shown that the redox potentials (E m’s) of the redox-active pheophytin a (Pheo) and the primary plastoquinone electron acceptor (QA) in photosystem II (PSII) of A. marina are higher than those in Chl a-containing PSII, to compensate for the smaller excitation energy of Chl d (Allakhverdiev et al., Proc Natl Acad Sci USA 107: 3924–3929, 2010; ibid. 108: 8054–8058, 2011). To clarify the mechanisms of these E m increases, in this study, we have investigated the molecular interactions of Pheo and QA in PSII core complexes from A. marina using Fourier transform infrared (FTIR) spectroscopy. Light-induced FTIR difference spectra upon single reduction of Pheo and QA showed that spectral features in the regions of the keto and ester C=O stretches and the chlorin ring vibrations of Pheo and in the CO/CC stretching region of the Q A semiquinone anion in A. marina are significantly different from those of the corresponding spectra in Chl a-containing cyanobacteria. These observations indicate that the molecular interactions, including the hydrogen bond interactions at the C=O groups, of these cofactors are modified in their binding sites of PSII proteins. From these results, along with the sequence information of the D1 and D2 proteins, it is suggested that A. marina tunes the E m’s of Pheo and QA by altering nearby hydrogen bond networks to modify the structures of the binding pockets of these cofactors.
Keywords: Chlorophyll d ; Pheophytin; Plastoquinone; Fourier transform infrared spectroscopy; Vibrational spectroscopy; Redox potential

Energy transfer in the chlorophyll f-containing cyanobacterium, Halomicronema hongdechloris, analyzed by time-resolved fluorescence spectroscopies by Seiji Akimoto; Toshiyuki Shinoda; Min Chen; Suleyman I. Allakhverdiev; Tatsuya Tomo (115-122).
We prepared thylakoid membranes from Halomicronema hongdechloris cells grown under white fluorescent light or light from far-red (740 nm) light-emitting diodes, and observed their energy-transfer processes shortly after light excitation. Excitation–relaxation processes were examined by steady-state and time-resolved fluorescence spectroscopies. Two time-resolved fluorescence techniques were used: time-correlated single photon counting and fluorescence up-conversion methods. The thylakoids from the cells grown under white light contained chlorophyll (Chl) a of different energies, but were devoid of Chl f. At room temperature, the excitation energy was equilibrated among the Chl a pools with a time constant of 6.6 ps. Conversely, the thylakoids from the cells grown under far-red light possessed both Chl a and Chl f. Two energy-transfer pathways from Chl a to Chl f were identified with time constants of 1.3 and 5.0 ps, and the excitation energy was equilibrated between the Chl a and Chl f pools at room temperature. We also examined the energy-transfer pathways from phycobilisome to the two photosystems under white-light cultivation.
Keywords: Energy transfer; Fluorescence; Light adaptation; Chlorophyll f ; Pigment-protein complex; Time-resolved spectroscopy

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 $${ ext{Q}}_{ ext{B}}^{ - }$$ Q B - ) 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 3Car(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 $$F_{ ext{m}}^{ ext{STF}}$$ F m STF /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 3Car(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 $${ ext{Q}}_{ ext{A}}^{ - } ;{ ext{to}};{ ext{Q}}_{ ext{B}}^{( - )}$$ Q A - to Q B ( - ) slower in alga as compared to leaf samples was elucidated by the dynamics of $${ ext{Q}}_{ ext{A}}^{ - } ,{ ext{ Q}}_{ ext{B}}^{ - }$$ Q A - , Q B - 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.
Keywords: Fluorescence yield; Single turnover flash; Photosystem II; Model simulation; Electron transfer; Dissipative energy losses; Proton transfer; Water oxidizing complex

In the present study, the influence of 50 and 100 µM CuSO4 was investigated starting from 3 h till 72 h treatment of 4-weeks Brassica napus plants. High CuSO4 concentrations in nutrient medium resulted in the rapid copper accumulation in plants, especially in roots, much slower and to lower degree in leaves. Copper excess induced early decrease in the leaf water content and temporary leaf wilting. The decrease in content of photosynthetic pigments became significant to 24 h of excessive copper treatments and reached 35 % decrease to 72 h, but there were no significant changes in maximum quantum efficiency of photosystem II photochemistry. The copper excess affected the expression of ten genes involved in heavy metal homeostasis and copper detoxification. The results showed the differential and organ-specific expression of most genes. The potential roles of copper-activated genes encoding heavy metal transporters (ZIP5, NRAMP4, YSL2, and MRP1), metallothioneins (MT1a and MT2b), low-molecular chelator synthesis enzymes (PCS1 and NAS2), and metallochaperones (CCS and HIPP06) in heavy metal homeostasis and copper ion detoxification were discussed. The highest increase in gene expression was shown for NRAMP4 in leaves in spite of relatively moderate Cu accumulation there. The opinion was advanced that the NRAMP4 activation can be considered among the early reactions in the defense of the photosystem II against copper excess.
Keywords: Brassica napus ; Copper detoxification; Copper excess; Photosynthetic pigments; Photosystem II photochemistry; Gene expression

Low PSI content limits the photoprotection of PSI and PSII in early growth stages of chlorophyll b-deficient wheat mutant lines by Marian Brestic; Marek Zivcak; Kristyna Kunderlikova; Oksana Sytar; Hongbo Shao; Hazem M. Kalaji; Suleyman I. Allakhverdiev (151-166).
In vivo analyses of electron and proton transport-related processes as well as photoprotective responses were carried out at different stages of growth in chlorophyll b (Chl b)-deficient mutant lines (ANK-32A and ANK-32B) and wild type (WT) of wheat (Triticum aestivum L.). In addition to a high Chl ab ratio, ANK mutants had a lower content of photo-oxidizable photosystem I (PSI, P m), and several parameters indicated a low PSI/PSII ratio. Moreover, simultaneous measurements of Chl fluorescence and P700 indicated a shift of balance between redox poise of the PSII acceptor side and the PSII donor side, with preferential reduction of the plastoquinone pool, resulting in an over reduced PSI acceptor side (high Φ NA values). This was the probable reason for PSI inactivation observed in the ANK mutants, but not in WT. In later growth phases, we observed partial relief of “chlorina symptoms,” toward WT. Measurements of ΔA 520 decay confirmed that, in early growth stages, the ANK mutants with low PSI content had a limited capacity to build up the transthylakoid proton gradient (ΔpH) needed to trigger non-photochemical quenching (NPQ) and to regulate the electron transport by cytochrome b 6/f. Later, the increase in the PSI/PSII ratio enabled ANK mutants to reach full NPQ, but neither over reduction of the PSI acceptor side nor PSI photoinactivation due to imbalance between the activity of PSII and PSI was mitigated. Thus, our results support the crucial role of proper regulation of linear electron transport in the protection of PSI against photoinhibition. Moreover, the ANK mutants of wheat showing the dynamic developmental changes in the PSI/PSII ratio are presented here as very useful models for further studies.
Keywords: Chlorina mutants; Wheat; Non-photochemical quenching; Chlorophyll fluorescence; Transthylakoid proton gradient; PSI photoinhibition

Features of temporal behavior of fluorescence recovery in Synechocystis sp. PCC6803 by E. G. Maksimov; K. E. Klementiev; E. A. Shirshin; G. V. Tsoraev; I. V. Elanskaya; V. Z. Paschenko (167-178).
Under high photon flux density of solar radiation, the photosynthetic apparatus can be damaged. To prevent this photodestruction, cyanobacteria developed special mechanisms of non-photochemical quenching (NPQ) of excitation energy in phycobilisomes. In Synechocystis, NPQ is triggered by the orange carotenoid protein (OCP), which is sensitive to blue-green illumination allowing it to bind to the phycobilisome reducing the flow of energy to the photosystems. Consequent decoupling of OCP and recovery of phycobilisome fluorescence in vivo is controlled by the so called fluorescence recovery protein (FRP). In this work, the role of the phycobilisome core components, apcD and apcF, in non-photochemical quenching and subsequent fluorescence recovery in the phycobilisomes of the cyanobacterium Synechocystis sp. PCC6803 has been investigated. Using a single photon counting technique, we have registered fluorescence decay spectra with picosecond time resolution during fluorescence recovery. In order to estimate the activation energy for the photocycle, spectroscopic studies in dependency on the temperature from 5 to 45 °C have been performed. It was found that fluorescence quenching and recovery were strongly temperature dependent for all strains exhibiting characteristic non-linear time courses. The rise of the fluorescence intensity during fluorescence recovery after NPQ can be completely described by the increase of the phycobilisome core fluorescence lifetime. It was shown that fluorescence recovery of apcD- and apcF-deficient mutants is characterized by a significantly lower activation energy barrier compared to wild type. This phenomenon indicates that apcD and apcF gene products may be required for proper interaction of FRP and OCP coupled to the phycobilisome core. In addition, we found that the rate of fluorescence recovery decreases with an increase of the non-photochemical quenching amplitude, probably due to depletion of substrate for the enzymatic reaction catalyzed by FRP.
Keywords: Orange carotenoid protein; Fluorescence recovery protein; Non-photochemical quenching; Phycobilisome; Fluorescence lifetime

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 ( $${F_{{ ext{o}}_{ ext{calc.}}^{^prime }}}$$ F o calc. ′ ) than those calculated according to the formula of Oxborough and Baker (Photosynth Res 54:135–142 1997) ( $${F_{{ ext{o}}_{ ext{calc.}}^{^prime } }}$$ F o calc. ′ ), 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.
Keywords: Arabidopsis ; Protective NPQ; Photoinhibition; Photosystem II; Photosystem I

Some filamentous cyanobacteria (including Anabaena) differentiate into heterocysts under nitrogen-depleted conditions. During differentiation, the phycobiliproteins and photosystem II in the heterocysts are gradually degraded. Nitrogen depletion induces changes in the pigment composition of both vegetative cells and heterocysts, which affect the excitation energy transfer processes. To investigate the changes in excitation energy transfer processes of Anabaena variabilis filaments grown in standard medium (BG11) and a nitrogen-free medium (BG110), we measured their steady-state absorption spectra, steady-state fluorescence spectra, and time-resolved fluorescence spectra (TRFS) at 77 K. TRFS were measured with a picosecond time-correlated single photon counting system. The pigment compositions of the filaments grown in BG110 changed throughout the growth period; the relative phycocyanin levels monotonically decreased, whereas the relative carotenoid (Car) levels decreased and then recovered to their initial value (at day 0), with formation of lower-energy Cars. Nitrogen starvation also altered the fluorescence kinetics of PSI; the fluorescence maximum of TRFS immediately after excitation occurred at 735, 740, and 730 nm after 4, 8, and 15 days growth in BG110, respectively. Based on these results, we discuss the excitation energy transfer dynamics of A. variabilis filaments under the nitrogen-depleted condition throughout the growth period.
Keywords: Energy transfer; Time-resolved fluorescence; Nitrogen depletion; Cyanobacteria

Differences in energy transfer of a cyanobacterium, Synechococcus sp. PCC 7002, grown in different cultivation media by Kenta Niki; Shimpei Aikawa; Makio Yokono; Akihiko Kondo; Seiji Akimoto (201-210).
Currently, cyanobacteria are regarded as potential biofuel sources. Large-scale cultivation of cyanobacteria in seawater is of particular interest because seawater is a low-cost medium. In the present study, we examined differences in light-harvesting and energy transfer processes in the cyanobacterium Synechococcus sp. PCC 7002 grown in different cultivation media, namely modified A medium (the optimal growth medium for Synechococcus sp. PCC 7002) and f/2 (a seawater medium). The concentrations of nitrate and phosphate ions were varied in both media. Higher nitrate ion and/or phosphate ion concentrations yielded high relative content of phycobilisome. The cultivation medium influenced the energy transfers within phycobilisome, from phycobilisome to photosystems, within photosystem II, and from photosystem II to photosystem I. We suggest that the medium also affects charge recombination at the photosystem II reaction center and formation of a chlorophyll-containing complex.
Keywords: Energy transfer; Fluorescence; Nitrogen deficiency; Phosphorus deficiency; Pigment–protein complex; Time-resolved spectroscopy

Photosynthetic organisms change the quantity and/or quality of their pigment–protein complexes and the interactions among these complexes in response to light conditions. In the present study, we analyzed light adaptation of the unicellular red alga Cyanidioschyzon merolae, whose pigment composition is similar to that of cyanobacteria because its phycobilisomes (PBS) lack phycoerythrin. C. merolae were grown under different light qualities, and their responses were measured by steady-state absorption, steady-state fluorescence, and picosecond time-resolved fluorescence spectroscopies. Cells were cultivated under four monochromatic light-emitting diodes (blue, green, yellow, and red), and changes in pigment composition and energy transfer were observed. Cells grown under blue and green light increased their relative phycocyanin levels compared with cells cultured under white light. Energy-transfer processes to photosystem I (PSI) were sensitive to yellow and red light. The contribution of direct energy transfer from PBS to PSI increased only under yellow light, while red light induced a reduction in energy transfer from photosystem II to PSI and an increase in energy transfer from light-harvesting chlorophyll protein complex I to PSI. Differences in pigment composition, growth, and energy transfer under different light qualities are discussed.
Keywords: Energy transfer; Light adaptation; Phycobilisome; Delayed fluorescence; Red alga; Cyanidioschyzon merolae

The slow S to M rise of chlorophyll a fluorescence reflects transition from state 2 to state 1 in the green alga Chlamydomonas reinhardtii by Sireesha Kodru; Tirupathi Malavath; Elsinraju Devadasu; Sreedhar Nellaepalli; Alexandrina Stirbet; Rajagopal Subramanyam; Govindjee (219-231).
The green alga Chlamydomonas (C.) reinhardtii is a model organism for photosynthesis research. State transitions regulate redistribution of excitation energy between photosystem I (PS I) and photosystem II (PS II) to provide balanced photosynthesis. Chlorophyll (Chl) a fluorescence induction (the so-called OJIPSMT transient) is a signature of several photosynthetic reactions. Here, we show that the slow (seconds to minutes) S to M fluorescence rise is reduced or absent in the stt7 mutant (which is locked in state 1) in C. reinhardtii. This suggests that the SM rise in wild type C. reinhardtii may be due to state 2 (low fluorescence state; larger antenna in PS I) to state 1 (high fluorescence state; larger antenna in PS II) transition, and thus, it can be used as an efficient and quick method to monitor state transitions in algae, as has already been shown in cyanobacteria (Papageorgiou et al. 1999, 2007; Kaňa et al. 2012). We also discuss our results on the effects of (1) 3-(3,4-dichlorophenyl)-1,4-dimethyl urea, an inhibitor of electron transport; (2) n-propyl gallate, an inhibitor of alternative oxidase (AOX) in mitochondria and of plastid terminal oxidase in chloroplasts; (3) salicylhydroxamic acid, an inhibitor of AOX in mitochondria; and (4) carbonyl cyanide p-trifluoromethoxyphenylhydrazone, an uncoupler of phosphorylation, which dissipates proton gradient across membranes. Based on the data presented in this paper, we conclude that the slow PSMT fluorescence transient in C. reinhardtii is due to the superimposition of, at least, two phenomena: qE dependent non-photochemical quenching of the excited state of Chl, and state transitions.
Keywords: Chlorophyll fluorescence; Light-harvesting complex; Photosystem I; Photosystem II; State transitions

Sll0751 and Sll1041 are involved in acid stress tolerance in Synechocystis sp. PCC 6803 by Hiroko Tahara; Ayumi Matsuhashi; Junji Uchiyama; Satoru Ogawa; Hisataka Ohta (233-242).
The ATP-binding cassette (ABC) transporter is a multi-subunit membrane protein complex involved in lipid transport and acid stress tolerance in the cyanobacterium Synechocystis sp. PCC 6803. This organism has two sets of three ABC transporter subunits: Slr1045 and Slr1344, Sll0751 and Sll1002, and Sll1001 and Sll1041. We previously found that Slr1045 is essential for survival under acid stress condition (Tahara et al. 2012). In the present study, we examined the participation of other ABC transporter subunits in acid stress tolerance using a deletion mutant series of Synechocystis sp. PCC 6803. Although Slr1344 is highly homologous to Slr1045, Δslr1344 cells were not susceptible to acid stress. Δsll0751 and Δsll1041 cells displayed acid stress sensitivity, whereas Δsll1001/sll1002 double mutant cells grew normally. Under high- and low-temperature stress conditions, the growth rate of Δslr1344 and Δsll1001/sll1002 cells did not differ from WT cells, whereas Δsll0751 and Δsll1041 cells showed significant growth retardation, as previously observed in Δslr1045 cells. Moreover, nile red staining showed more lipid accumulation in Δslr1045, Δsll0751, and Δsll1041 cells than in WT cells. These results suggest that Slr1045, Sll0751, and Sll1041 function together as a lipid transport complex in Synechocystis sp. PCC 6803 and are essential for growth under various stresses.
Keywords: Acid stress; ABC transporter; Synechocystis sp. PCC 6803

Genomic analysis of parallel-evolved cyanobacterium Synechocystis sp. PCC 6803 under acid stress by Junji Uchiyama; Yu Kanesaki; Naoya Iwata; Ryousuke Asakura; Kento Funamizu; Rizumu Tasaki; Mina Agatsuma; Hiroko Tahara; Ayumi Matsuhashi; Hirofumi Yoshikawa; Satoru Ogawa; Hisataka Ohta (243-254).
Experimental evolution is a powerful tool for clarifying phenotypic and genotypic changes responsible for adaptive evolution. In this study, we isolated acid-adapted Synechocystis sp. PCC 6803 (Synechocystis 6803) strains to identify genes involved in acid tolerance. Synechocystis 6803 is rarely found in habitants with pH < 5.75. The parent (P) strain was cultured in BG-11 at pH 6.0. We gradually lowered the pH of the medium from pH 6.0 to pH 5.5 over 3 months. Our adapted cells could grow in acid stress conditions at pH 5.5, whereas the parent cells could not. We performed whole-genome sequencing and compared the acid-adapted and P strains, thereby identifying 11 SNPs in the acid-adapted strains, including in Fo F1-ATPase. To determine whether the SNP genes responded to acid stress, we examined gene expression in the adapted strains using quantitative reverse-transcription polymerase chain reaction. sll0914, sll1496, sll0528, and sll1144 expressions increased under acid stress in the P strain, whereas sll0162, sll0163, slr0623, and slr0529 expressions decreased. There were no differences in the SNP genes expression levels between the P strain and two adapted strains, except for sll0528. These results suggest that SNPs in certain genes are involved in acid stress tolerance in Synechocystis 6803.
Keywords: Low pH; Stress response; Synechocystis sp. PCC 6803; Experimental evolution; Whole genome sequence

Acaryochloris marina MBIC 11017 possesses chlorophyll (Chl) d as a major Chl, which enables this organism to utilize far-red light for photosynthesis. Thus, the adaptation mechanism of far-red light utilization, including Chl d biosynthesis, has received much attention, though a limited number of reports on this subject have been published. To identify genes responsible for Chl d biosynthesis and adaptation to far-red light, molecular genetic analysis of A. marina was required. We developed a transformation system for A. marina and introduced expression vectors into A. marina. In this study, the high-frequency in vivo transposon mutagenesis system recently established by us was applied to A. marina. As a result, we obtained mutants with the transposon in their genomic DNA at various positions. By screening transposon-tagged mutants, we isolated a mutant (Y1 mutant) that formed a yellow colony on agar medium. In the Y1 mutant, the transposon was inserted into the gene encoding molybdenum cofactor biosynthesis protein A (MoaA). The Y1 mutant was functionally complemented by introducing the moaA gene or increasing the ammonium ion in the medium. These results indicate that the mutation of the moaA gene reduced nitrate reductase activity, which requires molybdenum cofactor, in the Y1 mutant. This is the first successful forward genetic analysis of A. marina, which will lead to the identification of genes responsible for adaptation to far-red light.
Keywords: Acaryochloris marina MBIC 11017; Chlorophyll d ; Cyanobacteria; Genetic functional complementation; Transposon mutagenesis system

Slr2019, lipid A transporter homolog, is essential for acidic tolerance in Synechocystis sp. PCC6803 by Ayumi Matsuhashi; Hiroko Tahara; Yutaro Ito; Junji Uchiyama; Satoru Ogawa; Hisataka Ohta (267-277).
Living organisms must defend themselves against various environmental stresses. Extracellular polysaccharide-producing cells exhibit enhanced tolerance toward adverse environmental stress. In Synechocystis sp. PCC6803 (Synechocystis), lipopolysaccharide (LPS) may play a role in this protection. To examine the relationship between stress tolerance of Synechocystis and LPS, we focused on Slr2019 because Slr2019 is homologous to MsbA in Escherichia coli, which is related to LPS synthesis. First, to obtain a defective mutant of LPS, we constructed the slr2019 insertion mutant (slr2019) strain. Sodium deoxycholate-polyacrylamide gel electrophoresis indicated that slr2019 strain did not synthesize normal LPS. Second, to clarify the participation of LPS in acid tolerance, wild type (WT) and slr2019 strain were grown under acid stress; slr2019 strain growth was significantly weaker than WT growth. Third, to examine influences on stress tolerance, slr2019 strain was grown under various stresses. Under salinity and temperature stress, slr2019 strain grew significantly slower than WT. To confirm cell morphology, cell shape and envelope of slr2019 strain were observed by transmission electron microscopy; slr2019 cells contained more electron-transparent bodies than WT cells. Finally, to confirm whether electron-transparent bodies are poly-3-hydroxybutyrate (PHB), slr2019 strain was stained with Nile Blue A, a PHB detector, and observed by fluorescence microscopy. The PHB granule content ratio of WT and slr2019 strain grown at BG-11 pH 8.0 was each 7.18 and 8.41 %. At pH 6.0, the PHB granule content ratio of WT and slr2019 strain was 2.99 and 2.60 %. However, the PHB granule content ratio of WT and slr2019 strain grown at BG-11N-reduced was 10.82 and 0.56 %. Because slr2019 strain significantly decreased PHB under BG-11N-reduced compared with WT, LPS synthesis may be related to PHB under particular conditions. These results indicated that Slr2019 is necessary for Synechocystis survival in various stresses.
Keywords: Acid stress; Lipopolysaccharide; slr2019 ; Stress tolerance; Synechocystis sp. PCC6803

The dynamics of the activity of catalase, ascorbate peroxidase, guaiacol peroxidase, and benzidine peroxidase, as well as the level of hydrogen peroxide in the vegetative organs of durum wheat (Triticum durum Desf.) cultivars was studied under long-term soil drought conditions. It was established that hydrogen peroxide generation occurred at early stages of stress in the tolerant variety Barakatli-95, whereas in the susceptible variety Garagylchyg-2 its significant amounts were accumulated only at later stages. Garagylchyg-2 shows a larger reduction of photochemical activity of PS II in both genotypes at all stages of ontogenesis under drought stress than Barakatli-95. The highest activity of catalase which plays a leading role in the neutralization of hydrogen peroxide was observed in the leaves and roots of the drought-tolerant variety Barakatli-95. Despite the fact that the protection system also includes peroxidases, the activity of these enzymes even after synthesis of their new portions is substantially lower compared with catalase. Native PAGE electrophoresis revealed the presence of one isoform of CAT, seven isoforms of APX, three isoforms of GPO, and three isoforms of BPO in the leaves, and also three isoforms of CAT, four isoforms of APX, two isoforms of GPO, and six isoforms of BPO in the roots of wheat. One isoform of CAT was found in the roots when water supply was normal and three isoforms were observed under drought conditions. Stress associated with long-term soil drought in the roots of wheat has led to an increase in the heterogeneity due to the formation of two new sedentary forms of catalase: CAT2 and CAT3.
Keywords: Triticum durum Desf.; Leaf; Root; Photosystem II; Antioxidant enzymes; Drought stress

Cadmium accumulation in chloroplasts and its impact on chloroplastic processes in barley and maize by Eugene A. Lysenko; Alexander A. Klaus; Natallia L. Pshybytko; Victor V. Kusnetsov (291-303).
Data on cadmium accumulation in chloroplasts of terrestrial plants are scarce and contradictory. We introduced CdSO4 in hydroponic media to the final concentrations 80 and 250 μM and studied the accumulation of Cd in chloroplasts of Hordeum vulgare and Zea mays. Barley accumulated more Cd in the chloroplasts as compared to maize, whereas in the leaves cadmium accumulation was higher in maize. The cadmium content in the chloroplasts of two species varied from 49 to 171 ng Cd/mg chlorophyll, which corresponds to one Cd atom per 728–2,540 chlorophyll molecules. Therefore, Mg2+ can be substituted by Cd2+ in a negligible amount of antenna chlorophylls only. The percentage of chloroplastic cadmium can be estimated as 0.21–1.32 % of all the Cd in a leaf. Photochemistry (F v/F m, ΦPSII, qP) was not influenced by Cd. Non-photochemical quenching of chlorophyll-excited state (NPQ) was greatly reduced in barley but not in maize. The decrease in NPQ was due to its fast relaxing component; the slow relaxing component rose slightly. In chloroplasts, Cd did not affect mRNA levels, but content of some photosynthetic proteins was reduced: slightly in the leaves of barley and heavily in the leaves of maize. In all analyzed C3-species, the effect of Cd on the content of photosynthetic proteins was mild or absent. This is most likely the first evidence of severe reduction of photosynthetic proteins in leaves of a Cd-treated C4-plant.
Keywords: Cadmium; Chloroplasts; mRNA; Proteins; Barley; Maize; Photosystem II activity

Investigations were carried to unravel mechanism(s) for higher tolerance of floating over submerged leaves of long leaf pondweed (Potamogeton nodosus Poir) against photoinhibition. Chloroplasts from floating leaves showed ~5- and ~6.4-fold higher Photosystem (PS) I (reduced dichlorophenol-indophenol → methyl viologen → O2) and PS II (H2O → parabenzoquine) activities over those from submerged leaves. The saturating rate (V max) of PS II activity of chloroplasts from floating and submerged leaves reached at ~600 and ~230 µmol photons m−2 s−1, respectively. Photosynthetic electron transport rate in floating leaves was over 5-fold higher than in submerged leaves. Further, floating leaves, as compared to submerged leaves, showed higher F v/F m (variable to maximum chlorophyll fluorescence, a reflection of PS II efficiency), as well as a higher potential to withstand photoinhibitory damage by high light (1,200 µmol photons m−2 s−1). Cells of floating leaves had not only higher mitochondria to chloroplast ratio, but also showed many mitochondria in close vicinity of chloroplasts. Electron transport (NADH → O2; succinate → O2) in isolated mitochondria of floating leaves was sensitive to both cyanide (CN) and salicylhydroxamic acid (SHAM), whereas those in submerged leaves were sensitive to CN, but virtually insensitive to SHAM, revealing the presence of alternative oxidase in mitochondria of floating, but not of submerged, leaves. Further, the potential of floating leaves to withstand photoinhibitory damage was significantly reduced in the presence of CN and SHAM, individually and in combination. Our experimental results establish that floating leaves possess better photosynthetic efficiency and capacity to withstand photoinhibition compared to submerged leaves; and mitochondria play a pivotal role in protecting photosynthetic machinery of floating leaves against photoinhibition, most likely by oxidation of NAD(P)H and reduction of O2.
Keywords: Chlorophyll a fluorescence; CN-resistant alternative oxidase pathway; CN-sensitive cytochrome oxidase pathway; Chloroplast-mitochondria interaction; Photoinhibition; Potamogeton nodosus

Ferredoxin-NAD(P)+ oxidoreductases ([EC], [EC], FNRs) from green sulfur bacteria, purple non-sulfur bacteria and most of Firmicutes, such as Bacillus subtilis (BsFNR) are homo-dimeric flavoproteins homologous to bacterial NADPH-thioredoxin reductase. These FNRs contain two unique aromatic residues stacked on the si- and re-face of the isoalloxazine ring moiety of the FAD prosthetic group whose configurations are often found among other types of flavoproteins including plant-type FNR and flavodoxin, but not in bacterial NADPH-thioredoxin reductase. To investigate the role of the si-face Tyr50 residue in BsFNR, we replaced Tyr50 with Gly, Ser, and Trp and examined its spectroscopic properties and enzymatic activities in the presence of NADPH and ferredoxin (Fd) from B. subtilis (BsFd). The replacement of Tyr50 to Gly (Y50G), Ser (Y50S), and Trp (Y50W) in BsFNR resulted in a blue shift of the FAD transition bands. The Y50G and Y50S mutations enhanced the FAD fluorescence emission, whereas those of the wild type and Y50W mutant were quenched. All three mutants decreased thermal stabilities compared to wild type. Using a diaphorase assay, the k cat values for the Y50G and Y50S mutants in the presence of NADPH and ferricyanide were decreased to less than 5 % of the wild type activity. The Y50W mutant retained approximately 20 % reactivity in the diaphorase assay and BsFd-dependent cytochrome c reduction assay relative to wild type. The present results suggest that Tyr50 modulates the electronic properties and positioning of the prosthetic group.
Keywords: Ferredoxin; Flavin adenine dinucleotide; NADPH; Tyrosine

Cyanofuels: biofuels from cyanobacteria. Reality and perspectives by Fariza Sarsekeyeva; Bolatkhan K. Zayadan; Aizhan Usserbaeva; Vladimir S. Bedbenov; Maria A. Sinetova; Dmitry A. Los (329-340).
Cyanobacteria are represented by a diverse group of microorganisms that, by virtue of being a part of marine and freshwater phytoplankton, significantly contribute to the fixation of atmospheric carbon via photosynthesis. It is assumed that ancient cyanobacteria participated in the formation of earth’s oil deposits. Biomass of modern cyanobacteria may be converted into bio-oil by pyrolysis. Modern cyanobacteria grow fast; they do not compete for agricultural lands and resources; they efficiently convert excessive amounts of CO2 into biomass, thus participating in both carbon fixation and organic chemical production. Many cyanobacterial species are easier to genetically manipulate than eukaryotic algae and other photosynthetic organisms. Thus, the cyanobacterial photosynthesis may be directed to produce carbohydrates, fatty acids, or alcohols as renewable sources of biofuels. Here we review the recent achievements in the developments and production of cyanofuels—biofuels produced from cyanobacterial biomass.
Keywords: Biofuels; Biomass; Cyanobacteria; Cyanofuels; Fatty acids; Photosynthesis

The results of homology modeling of HydSL, a NiFe-hydrogenase from purple sulfur bacterium Thiocapsa roseopersicina BBS, and deep-water bacterium Alteromonas macleodii deep ecotype are presented in this work. It is shown that the models have larger confidence level than earlier published ones; full-size models of these enzymes are presented for the first time. The C-end fragment of small subunit of T. roseopersicina hydrogenase is shown to have random orientation in relation to the main protein globule. The obtained models of this enzyme have a large number of ion pairs, as well as thermostable HydSL hydrogenase from Allochromatium vinosum, in contrast to thermostable HydSL hydrogenase from Alt. macleodii and thermolabile HydAB hydrogenase from Desulfovibrio vulgaris. The possible determinant of oxygen stability of studied hydrogenases could be the lack of several intramolecular tunnels. Hydrophobic and electrostatic surfaces were mapped in order to find out possible pathways of coupling hydrogenase to electron-transferring chains, as well as methods for construction of artificial photobiohydrogen-producing systems.
Keywords: Homology modeling; Hydrogenases; Thiocapsa roseopersicina ; Alteromonas macleodii ; Hydrogen fuel cells