BBA - Bioenergetics (v.1857, #1)

The chloroplast must regulate supply of reducing equivalents and ATP to meet rapid changes in downstream metabolic demands. Cyclic electron flow around photosystem I (CEF) is proposed to balance the ATP/NADPH budget by using reducing equivalents to drive plastoquinone reduction, leading to the generation of proton motive force and subsequent ATP synthesis. While high rates of CEF have been observed in vivo, isolated thylakoids show only very slow rates, suggesting that the activity of a key complex is lost or down-regulated upon isolation. We show that isolation of thylakoids while in the continuous presence of reduced thiol reductant dithiothreitol (DTT), but not oxidized DTT, maintains high CEF activity through an antimycin A sensitive ferredoxin:quinone reductase (FQR). Maintaining low concentrations (~ 2 mM) of reduced DTT while modulating the concentration of oxidized DTT leads to reversible activation/inactivation of CEF with an apparent midpoint potential of − 306 mV (±10 mV) and n  = 2, consistent with redox modulation of a thiol/disulfide couple and thioredoxin-mediated regulation of the plastoquinone reductase involved in the antimycin A-sensitive pathway, possibly at the level of the PGRL1 protein. Based on proposed differences in regulatory modes, we propose that the FQR and NADPH:plastoquinone oxidoreductase (NDH) pathways for CEF are activated under different conditions and fulfill different roles in chloroplast energy balance.
Keywords: Spinacia oleracea; Photosynthesis; Energy balance; Cyclic electron flow; Redox regulation;

Unraveling the electron transfer processes of a nanowire protein from Geobacter sulfurreducens by Mónica N. Alves; Ana P. Fernandes; Carlos A. Salgueiro; Catarina M. Paquete (7-13).
The extracellular electron transfer metabolism of Geobacter sulfurreducens is sustained by several multiheme c-type cytochromes. One of these is the dodecaheme cytochrome GSU1996 that belongs to a new sub-class of c-type cytochromes. GSU1996 is composed by four similar triheme domains (A–D). The C-terminal half of the molecule encompasses the domains C and D, which are connected by a small linker and the N-terminal half of the protein contains two domains (A and B) that form one structural unit. It was proposed that this protein works as an electrically conductive device in G. sulfurreducens, transferring electrons within the periplasm or to outer-membrane cytochromes. In this work, a novel strategy was applied to characterize in detail the thermodynamic and kinetic properties of the hexaheme fragment CD of GSU1996. This characterization revealed the electron transfer process of GSU1996 for the first time, showing that a heme at the edge of the C-terminal of the protein is thermodynamic and kinetically competent to receive electrons from physiological redox partners. This information contributes towards understanding how this new sub-class of cytochromes functions as nanowires, and also increases the current knowledge of the extracellular electron transfer mechanisms in G. sulfurreducens.Display Omitted
Keywords: Multiheme cytochromes; Geobacter; Nanowires; Electron transfer; Extracellular respiration;

Mitochondrial ADP/ATP carriers catalyze the equimolar exchange of ADP and ATP across the mitochondrial inner membrane. Structurally, they consist of three homologous domains with a single substrate binding site. They alternate between a cytoplasmic and matrix state in which the binding site is accessible to these compartments for binding of ADP or ATP. It has been proposed that cycling between states occurs by disruption and formation of a matrix and cytoplasmic salt bridge network in an alternating way, but formation of the latter has not been shown experimentally. Here, we show that state-dependent formation of the cytoplasmic salt bridge network can be demonstrated by measuring the effect of mutations on the thermal stability of detergent-solubilized carriers locked in a specific state. For this purpose, mutations were made to increase or decrease the overall interaction energy of the cytoplasmic network. When locked in the cytoplasmic state by the inhibitor carboxyatractyloside, the thermostabilities of the mutant and wild-type carriers were similar, but when locked in the matrix state by the inhibitor bongkrekic acid, they correlated with the predicted interaction energy of the cytoplasmic network, demonstrating its formation. Changing the interaction energy of the cytoplasmic network also had a profound effect on the kinetics of transport, indicating that formation of the network is a key step in the transport cycle. These results are consistent with a unique alternating access mechanism that involves the simultaneous rotation of the three domains around a central translocation pathway.Display Omitted
Keywords: Adenine nucleotide translocase; Membrane protein; Substrate exchange; Thermostability; Transport protein;

Estimation of the driving force for dioxygen formation in photosynthesis by Håkan Nilsson; Laurent Cournac; Fabrice Rappaport; Johannes Messinger; Jérôme Lavergne (23-33).
Photosynthetic water oxidation to molecular oxygen is carried out by photosystem II (PSII) over a reaction cycle involving four photochemical steps that drive the oxygen-evolving complex through five redox states Si (i = 0,…, 4). For understanding the catalytic strategy of biological water oxidation it is important to elucidate the energetic landscape of PSII and in particular that of the final S4  → S0 transition. In this short-lived chemical step the four oxidizing equivalents accumulated in the preceding photochemical events are used up to form molecular oxygen, two protons are released and at least one substrate water molecule binds to the Mn4CaO5 cluster. In this study we probed the probability to form S4 from S0 and O2 by incubating YD-less PSII in the S0 state for 2–3 days in the presence of 18O2 and H2 16O. The absence of any measurable 16,18O2 formation by water-exchange in the S4 state suggests that the S4 state is hardly ever populated. On the basis of a detailed analysis we determined that the equilibrium constant K of the S4  → S0 transition is larger than 1.0 × 107 so that this step is highly exergonic. We argue that this finding is consistent with current knowledge of the energetics of the S0 to S4 reactions, and that the high exergonicity is required for the kinetic efficiency of PSII.Display Omitted
Keywords: Photosystem II; Water-oxidizing complex (WOC); Oxygen-evolving complex (OEC); Equilibrium constant for S4  → S0 transition;

Specific degradation of phosphatidylglycerol is necessary for proper mitochondrial morphology and function by Lucia Pokorná; Petra Čermáková; Anton Horváth; Matthew G. Baile; Steven M. Claypool; Peter Griač; Jan Malínský; Mária Balážová (34-45).
In yeast, phosphatidylglycerol (PG) is a minor phospholipid under standard conditions; it can be utilized for cardiolipin (CL) biosynthesis by CL synthase, Crd1p, or alternatively degraded by the phospholipase Pgc1p. The Saccharomyces cerevisiae deletion mutants crd1Δ and pgc1Δ both accumulate PG. Based on analyses of the phospholipid content of pgc1Δ and crd1Δ yeast, we revealed that in yeast mitochondria, two separate pools of PG are present, which differ in their fatty acid composition and accessibility for Pgc1p-catalyzed degradation. In contrast to CL-deficient crd1Δ yeast, the pgc1Δ mutant contains normal levels of CL. This makes the pgc1Δ strain a suitable model to study the effect of accumulation of PG per se. Using fluorescence microscopy, we show that accumulation of PG with normal levels of CL resulted in increased fragmentation of mitochondria, while in the absence of CL, accumulation of PG led to the formation of large mitochondrial sheets. We also show that pgc1Δ mitochondria exhibited increased respiration rates due to increased activity of cytochrome c oxidase. Taken together, our results indicate that not only a lack of anionic phospholipids, but also excess PG, or unbalanced ratios of anionic phospholipids in mitochondrial membranes, have harmful consequences on mitochondrial morphology and function.
Keywords: Yeast; Phosphatidylglycerol; Mitochondria; Morphology; Respiration;

Fluorescence Lifetime Imaging Microscopy (FLIM) has been applied to plants, algae and cyanobacteria, in which excitation laser conditions affect the chlorophyll fluorescence lifetime due to several mechanisms. However, the dependence of FLIM data on input laser power has not been quantitatively explained by absolute excitation probabilities under actual imaging conditions. In an effort to distinguish between photosystem I and photosystem II (PSI and PSII) in microscopic images, we have obtained dependence of FLIM data on input laser power from a filamentous cyanobacterium Anabaena variabilis and single cellular green alga Parachlorella kessleri. Nitrogen-fixing cells in A. variabilis, heterocysts, are mostly visualized as cells in which short-lived fluorescence (≤ 0.1 ns) characteristic of PSI is predominant. The other cells in A. variabilis (vegetative cells) and P. kessleri cells show a transition in the status of PSII from an open state with the maximal charge separation rate at a weak excitation limit to a closed state in which charge separation is temporarily prohibited by previous excitation(s) at a relatively high laser power. This transition is successfully reproduced by a computer simulation with a high fidelity to the actual imaging conditions. More details in the fluorescence from heterocysts were examined to assess possible functions of PSII in the anaerobic environment inside the heterocysts for the nitrogen-fixing enzyme, nitrogenase. Photochemically active PSII:PSI ratio in heterocysts is tentatively estimated to be typically below our detection limit or at most about 5% in limited heterocysts in comparison with that in vegetative cells.Display Omitted
Keywords: Photosystem II; Photosystem I; Chlorophyll fluorescence; Fluorescence lifetime imaging microscopy; Heterocystous cyanobacteria; Green algae;

Depletion of the “gamma-type carbonic anhydrase-like” subunits of complex I affects central mitochondrial metabolism in Arabidopsis thaliana by Steffanie Fromm; Jennifer Göing; Christin Lorenz; Christoph Peterhänsel; Hans-Peter Braun (60-71).
“Gamma-type carbonic anhydrase-like” (CAL) proteins form part of complex I in plants. Together with “gamma carbonic anhydrase” (CA) proteins they form an extra domain which is attached to the membrane arm of complex I on its matrix exposed side. In Arabidopsis two CAL and three CA proteins are present, termed CAL1, CAL2, CA1, CA2 and CA3. It has been proposed that the carbonic anhydrase domain of complex I is involved in a process mediating efficient recycling of mitochondrial CO2 for photosynthetic carbon fixation which is especially important during growth conditions causing increased photorespiration. Depletion of CAL proteins has been shown to significantly affect plant development and photomorphogenesis. To better understand CAL function in plants we here investigated effects of CAL depletion on the mitochondrial compartment. In mutant lines and cell cultures complex I amount was reduced by 90–95% but levels of complexes III and V were unchanged. At the same time, some of the CA transcripts were less abundant. Proteome analysis of CAL depleted cells revealed significant reduction of complex I subunits as well as proteins associated with photorespiration, but increased amounts of proteins participating in amino acid catabolism and stress response reactions. Developmental delay of the mutants was slightly alleviated if plants were cultivated at high CO2. Profiling of selected metabolites revealed defined changes in intermediates of the citric acid cycle and amino acid catabolism. It is concluded that CAL proteins are essential for complex I assembly and that CAL depletion specifically affects central mitochondrial metabolism.
Keywords: Arabidopsis thaliana; Complex I; Mitochondrial metabolism; Proteomics; Respiratory chain; Carbonic anhydrase;

The expression of UCP3 directly correlates to UCP1 abundance in brown adipose tissue by Karolina E. Hilse; Anastasia V. Kalinovich; Anne Rupprecht; Alina Smorodchenko; Ute Zeitz; Katrin Staniek; Reinhold G. Erben; Elena E. Pohl (72-78).
UCP1 and UCP3 are members of the uncoupling protein (UCP) subfamily and are localized in the inner mitochondrial membrane. Whereas UCP1's central role in non-shivering thermogenesis is acknowledged, the function and even tissue expression pattern of UCP3 are still under dispute. Because UCP3 properties regarding transport of protons are qualitatively identical to those of UCP1, its expression in brown adipose tissue (BAT) alongside UCP1 requires justification. In this work, we tested whether any correlation exists between the expression of UCP1 and UCP3 in BAT by quantification of protein amounts in mouse tissues at physiological conditions, in cold-acclimated and UCP1 knockout mice. Quantification using recombinant UCP3 revealed that the UCP3 amount in BAT (0.51 ng/(μg total tissue protein)) was nearly one order of magnitude higher than that in muscles and heart. Cold-acclimated mice showed an approximate three-fold increase in UCP3 abundance in BAT in comparison to mice in thermoneutral conditions. Surprisingly, we found a significant decrease of UCP3 in BAT of UCP1 knockout mice, whereas the protein amount in skeletal and heart muscles remained constant. UCP3 abundance decreased even more in cold-acclimated UCP1 knockout mice. Protein quantification in UCP3 knockout mice revealed no compensatory increase in UCP1 or UCP2 expression. Our results do not support the participation of UCP3 in thermogenesis in the absence of UCP1 in BAT, but clearly demonstrate the correlation in abundance between both proteins. The latter is important for understanding UCP3's function in BAT.
Keywords: Recombinant protein; Anti-UCP3 antibody; UCP3 knockout mice; Cold-acclimated mice; Skeletal muscles; Uncoupling protein 2;

The N-terminal domain of Lhcb proteins is critical for recognition of the LHCII kinase by Wu Liu; Wenfeng Tu; Yang Liu; Ruixue Sun; Cheng Liu; Chunhong Yang (79-88).
The light-harvesting chlorophyll (Chl) a/b complex of photosystem (PS) II (LHCII) plays important roles in the distribution of the excitation energy between the two PSs in the thylakoid membrane during state transitions. In this process, LHCII, homo- or heterotrimers composed of Lhcb1–3, migrate between PSII and PSI depending on the phosphorylation status of Lhcb1 and Lhcb2. We have studied the mechanisms of the substrate recognition of a thylakoid threonine kinase using reconstituted site-directed trimeric Lhcb protein–pigment complex mutants. Mutants lacking the positively charged residues R/K upstream of phosphorylation site (Thr) in the N-terminal domain of Lhcb1 were no longer phosphorylated. Besides, the length of the peptide upstream of the phosphorylated site (Thr) is also crucial for Lhcb phosphorylation in vitro. Furthermore, the two N-terminal residues of Lhcb appear to play a key role in the phosphorylation kinetics because Lhcb with N-terminal RR was phosphorylated much faster than with RK. Therefore, we conclude that the substrate recognition of the LHCII kinase is determined to a large extent by the N-terminal sequence of the Lhcb proteins. The study provides new insights into the interactions of the Lhcb proteins with the LHCII kinase.
Keywords: Light harvesting complex; Kinase; N-terminal; Protein interactions;

Dimerization interface and dynamic properties of yeast IF1 revealed by Site-Directed Spin Labeling EPR spectroscopy by Nolwenn Le Breton; Tiona Adrianaivomananjaona; Guillaume Gerbaud; Emilien Etienne; Elena Bisetto; Alain Dautant; Bruno Guigliarelli; Francis Haraux; Marlène Martinho; Valérie Belle (89-97).
The mitochondrial ATPase inhibitor, IF1, regulates the activity of the mitochondrial ATP synthase. The oligomeric state of IF1 related to pH is crucial for its inhibitory activity. Although extensive structural studies have been performed to characterize the oligomeric states of bovine IF1, only little is known concerning those of yeast IF1. While bovine IF1 can be found as an inhibitory dimer at low pH and a non-inhibitory tetramer at high pH, a monomer/dimer equilibrium has been described for yeast IF1, high pH values favoring the monomeric state. Combining different strategies involving the grafting of nitroxide spin labels combined with Electron Paramagnetic Resonance (EPR) spectroscopy, the present study brings the first structural characterization, at the residue level, of yeast IF1 in its dimeric form. The results show that the dimerization interface involves the central region of the peptide revealing that the dimer corresponds to a non-inhibitory state. Moreover, we demonstrate that the C-terminal region of the peptide is highly dynamic and that this segment is probably folded back onto the central region. Finally, the pH-dependence of the inter-label distance distribution has been observed indicating a conformational change between two structural states in the dimer.Display Omitted
Keywords: ATP synthase; IF1 inhibitory peptide; Yeast; Dimerization interface; Protein dynamics;

The effect of a C298D mutation in CaHydA [FeFe]-hydrogenase: Insights into the protein-metal cluster interaction by EPR and FTIR spectroscopic investigation by Simone Morra; Sara Maurelli; Mario Chiesa; David W. Mulder; Michael W. Ratzloff; Elio Giamello; Paul W. King; Gianfranco Gilardi; Francesca Valetti (98-106).
A conserved cysteine located in the signature motif of the catalytic center (H-cluster) of [FeFe]-hydrogenases functions in proton transfer. This residue corresponds to C298 in Clostridium acetobutylicum CaHydA. Despite the chemical and structural difference, the mutant C298D retains fast catalytic activity, while replacement with any other amino acid causes significant activity loss. Given the proximity of C298 to the H-cluster, the effect of the C298D mutation on the catalytic center was studied by continuous wave (CW) and pulse electron paramagnetic resonance (EPR) and by Fourier transform infrared (FTIR) spectroscopies.Comparison of the C298D mutant with the wild type CaHydA by CW and pulse EPR showed that the electronic structure of the center is not altered. FTIR spectroscopy confirmed that absorption peak values observed in the mutant are virtually identical to those observed in the wild type, indicating that the H-cluster is not generally affected by the mutation. Significant differences were observed only in the inhibited state Hox–CO: the vibrational modes assigned to the COexo and Fed-CO in this state are shifted to lower values in C298D, suggesting different interaction of these ligands with the protein moiety when C298 is changed to D298. More relevant to the catalytic cycle, the redox equilibrium between the Hox and Hred states is modified by the mutation, causing a prevalence of the oxidized state.This work highlights how the interactions between the protein environment and the H-cluster, a dynamic closely interconnected system, can be engineered and studied in the perspective of designing bio-inspired catalysts and mimics.Display Omitted
Keywords: [FeFe]-hydrogenase; Proton transfer; EPR; HYSCORE; FTIR;

Characterization of red-shifted phycobilisomes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris by Yaqiong Li; Yuankui Lin; Christopher J. Garvey; Debra Birch; Robert W. Corkery; Patrick C. Loughlin; Hugo Scheer; Robert D. Willows; Min Chen (107-114).
Phycobilisomes are the main light-harvesting protein complexes in cyanobacteria and some algae. It is commonly accepted that these complexes only absorb green and orange light, complementing chlorophyll absorbance. Here, we present a new phycobilisome derived complex that consists only of allophycocyanin core subunits, having red-shifted absorption peaks of 653 and 712 nm. These red-shifted phycobiliprotein complexes were isolated from the chlorophyll f-containing cyanobacterium, Halomicronema hongdechloris, grown under monochromatic 730 nm-wavelength (far-red) light. The 3D model obtained from single particle analysis reveals a double disk assembly of 120–145 Å with two α/β allophycocyanin trimers fitting into the two separated disks. They are significantly smaller than typical phycobilisomes formed from allophycocyanin subunits and core-membrane linker proteins, which fit well with a reduced distance between thylakoid membranes observed from cells grown under far-red light. Spectral analysis of the dissociated and denatured phycobiliprotein complexes grown under both these light conditions shows that the same bilin chromophore, phycocyanobilin, is exclusively used. Our findings show that red-shifted phycobilisomes are required for assisting efficient far-red light harvesting. Their discovery provides new insights into the molecular mechanisms of light harvesting under extreme conditions for photosynthesis, as well as the strategies involved in flexible chromatic acclimation to diverse light conditions.Display Omitted
Keywords: Phycobilisome; Complementary chromatic acclimation; Far-red light; Small angle neutron scattering; Photosynthesis; Cyanobacteria;

Circularly polarized luminescence (CPL) spectroscopy is an established but relatively little-used technique that monitors the chirality of an emission. When applied to photosynthetic pigment assemblies, we find that CPL provides sensitive and detailed information on low-energy exciton states, reflecting the interactions, site energies and geometries of interacting pigments. CPL is the emission analog of circular dichroism (CD) and thus spectra explore the optical activity only of fluorescent states of the pigment-protein complex and consequently the nature of the lowest-energy excited states (trap states), whose study is a critical area of photosynthesis research. In this work, we develop the new approach of temperature-dependent CPL spectroscopy, over the 2–120 K temperature range, and apply it to the CP43 proximal antenna protein of photosystem II. Our results confirm strong excitonic interactions for at least one of the two well-established emitting states of CP43 named “A” and “B”. Previous structure-based models of CP43 spectra are evaluated in the light of the new CPL data. Our analysis supports the assignments of Shibata et al. [Shibata et al. J. Am. Chem. Soc. 135 (2013) 6903–6914], particularly for the highly-delocalized B-state. This state dominates CPL spectra and is attributed predominantly to chlorophyll a's labeled Chl 634 and Chl 636 (alternatively labeled Chl 43 and 45 by Shibata et al.). The absence of any CPL intensity in intramolecular vibrational sidebands associated with the delocalized “B” excited state is attributed to the dynamic localization of intramolecular vibronic transitions.Display Omitted
Keywords: Photosystem II; Fluorescence; Lowest excited states; Circular dichroism; Circularly polarized luminescence; Dynamic localization;