BBA - Bioenergetics (v.1858, #4)

Atypical composition and structure of the mitochondrial dimeric ATP synthase from Euglena gracilis by K.N. Sathish Yadav; Héctor V. Miranda-Astudillo; Lilia Colina-Tenorio; Fabrice Bouillenne; Hervé Degand; Pierre Morsomme; Diego González-Halphen; Egbert J. Boekema; Pierre Cardol (267-275).
Mitochondrial respiratory-chain complexes from Euglenozoa comprise classical subunits described in other eukaryotes (i.e. mammals and fungi) and subunits that are restricted to Euglenozoa (e.g. Euglena gracilis and Trypanosoma brucei). Here we studied the mitochondrial F1FO-ATP synthase (or Complex V) from the photosynthetic eukaryote E. gracilis in detail. The enzyme was purified by a two-step chromatographic procedure and its subunit composition was resolved by a three-dimensional gel electrophoresis (BN/SDS/SDS). Twenty-two different subunits were identified by mass-spectrometry analyses among which the canonical α, β, γ, δ, ε, and OSCP subunits, and at least seven subunits previously found in Trypanosoma. The ADP/ATP carrier was also associated to the ATP synthase into a dimeric ATP synthasome. Single-particle analysis by transmission electron microscopy of the dimeric ATP synthase indicated that the structures of both the catalytic and central rotor parts are conserved while other structural features are original. These new features include a large membrane-spanning region joining the monomers, an external peripheral stalk and a structure that goes through the membrane and reaches the inter membrane space below the c-ring, the latter having not been reported for any mitochondrial F-ATPase.
Keywords: Euglenozoa; Trypanosomatidae; Dimeric mitochondrial complex V; F1FO ATP synthase; Electron microscopy; ATP synthasome;

Flux balance analysis of photoautotrophic metabolism: Uncovering new biological details of subsystems involved in cyanobacterial photosynthesis by Xiao Qian; Min Kyung Kim; G. Kenchappa Kumaraswamy; Ananya Agarwal; Desmond S. Lun; G. Charles Dismukes (276-287).
We have constructed and experimentally tested a comprehensive genome-scale model of photoautotrophic growth, denoted iSyp821, for the cyanobacterium Synechococcus sp. PCC 7002. iSyp821 incorporates a variable biomass objective function (vBOF), in which stoichiometries of the major biomass components vary according to light intensity. The vBOF was constrained to fit the measured cellular carbohydrate/protein content under different light intensities. iSyp821 provides rigorous agreement with experimentally measured cell growth rates and inorganic carbon uptake rates as a function of light intensity. iSyp821 predicts two observed metabolic transitions that occur as light intensity increases: 1) from PSI-cyclic to linear electron flow (greater redox energy), and 2) from carbon allocation as proteins (growth) to carbohydrates (energy storage) mode. iSyp821 predicts photoautotrophic carbon flux into 1) a hybrid gluconeogenesis-pentose phosphate (PP) pathway that produces glycogen by an alternative pathway than conventional gluconeogenesis, and 2) the photorespiration pathway to synthesize the essential amino acid, glycine. Quantitative fluxes through both pathways were verified experimentally by following the kinetics of formation of 13C metabolites from 13CO2 fixation. iSyp821 was modified to include changes in gene products (enzymes) from experimentally measured transcriptomic data and applied to estimate changes in concentrations of metabolites arising from nutrient stress. Using this strategy, we found that iSyp821 correctly predicts the observed redistribution pattern of carbon products under nitrogen depletion, including decreased rates of CO2 uptake, amino acid synthesis, and increased rates of glycogen and lipid synthesis.
Keywords: Flux balance analysis; Carbon partitioning; Cyanobacteria; Gluconeogenesis-pentose phosphate (PP) pathway; Metabolism; Photorespiration; Nitrogen deprivation; Transcriptomic; Synechococcus 7002;

Probing the excitonic landscape of the Chlorobaculum tepidum Fenna-Matthews-Olson (FMO) complex: a mutagenesis approach by Rafael G. Saer; Valentyn Stadnytskyi; Nikki C. Magdaong; Carrie Goodson; Sergei Savikhin; Robert E. Blankenship (288-296).
In this paper we report the steady-state optical properties of a series of site-directed mutants in the Fenna-Matthews-Olson (FMO) complex of Chlorobaculum tepidum, a photosynthetic green sulfur bacterium. The FMO antenna complex has historically been used as a model system for energy transfer due to the water-soluble nature of the protein, its stability at room temperature, as well as the availability of high-resolution structural data. Eight FMO mutants were constructed with changes in the environment of each of the bacteriochlorophyll a pigments found within each monomer of the homotrimeric FMO complex. Our results reveal multiple changes in low temperature absorption, as well as room temperature CD in each mutant compared to the wild-type FMO complex. These datasets were subsequently used to model the site energies of each pigment in the FMO complex by employing three different Hamiltonians from the literature. This enabled a basic approximation of the site energy shifts imparted on each pigment by the changed amino acid residue. These simulations suggest that, while the three Hamiltonians used in this work provide good fits to the wild-type FMO absorption spectrum, further efforts are required to obtain good fits to the mutant minus wild-type absorption difference spectra. This demonstrates that the use of FMO mutants can be a valuable tool to refine and iterate the current models of energy transfer in this system.Display Omitted
Keywords: Fenna-Matthews-Olson; Exciton; Photosynthesis; Site-directed mutagenesis; Spectroscopy; Bacteriohlorophyll;

Unveiling the excited state energy transfer pathways in peridinin-chlorophyll a-protein by ultrafast multi-pulse transient absorption spectroscopy by Kipras Redeckas; Vladislava Voiciuk; Donatas Zigmantas; Roger G. Hiller; Mikas Vengris (297-307).
Time-resolved multi-pulse methods were applied to investigate the excited state dynamics, the interstate couplings, and the excited state energy transfer pathways between the light-harvesting pigments in peridinin-chlorophyll a-protein (PCP). The utilized pump-dump-probe techniques are based on perturbation of the regular PCP energy transfer pathway. The PCP complexes were initially excited with an ultrashort pulse, resonant to the S0  → S2 transition of the carotenoid peridinin. A portion of the peridinin-based emissive intramolecular charge transfer (ICT) state was then depopulated by applying an ultrashort NIR pulse that perturbed the interaction between S1 and ICT states and the energy flow from the carotenoids to the chlorophylls. The presented data indicate that the peridinin S1 and ICT states are spectrally distinct and coexist in an excited state equilibrium in the PCP complex. Moreover, numeric analysis of the experimental data asserts ICT → Chl-a as the main energy transfer pathway in the photoexcited PCP systems.Display Omitted
Keywords: Peridinin-chlorophyll a-protein; Pump-probe; Pump-dump-probe; Intramolecular charge transfer; Excited state equilibrium; Excitation energy transfer;

The cyanobacterial Fluorescence Recovery Protein has two distinct activities: Orange Carotenoid Protein amino acids involved in FRP interaction by Adrien Thurotte; Céline Bourcier de Carbon; Adjélé Wilson; Léa Talbot; Sandrine Cot; Rocio López-Igual; Diana Kirilovsky (308-317).
To deal with fluctuating light condition, cyanobacteria have developed a photoprotective mechanism which, under high light conditions, decreases the energy arriving at the photochemical centers. It relies on a photoswitch, the Orange Carotenoid Protein (OCP). Once photoactivated, OCP binds to the light harvesting antenna, the phycobilisome (PBS), and triggers the thermal dissipation of the excess energy absorbed. Deactivation of the photoprotective mechanism requires the intervention of a third partner, the Fluorescence Recovery Protein (FRP). FRP by interacting with the photoactivated OCP accelerates its conversion to the non-active form and its detachment from the phycobilisome. We have studied the interaction of FRP with free and phycobilisome-bound OCP. Several OCP variants were constructed and characterized. In this article we show that OCP amino acid F299 is essential and D220 important for OCP deactivation mediated by FRP. Mutations of these amino acids did not affect FRP activity as helper to detach OCP from phycobilisomes. In addition, while mutated R60L FRP is inactive on OCP deactivation, its activity on the detachment of the OCP from the phycobilisomes is not affected. Thus, our results demonstrate that FRP has two distinct activities: it accelerates OCP detachment from phycobilisomes and then it helps deactivation of the OCP. They also suggest that different OCP and FRP amino acids could be involved in these two activities.
Keywords: Cyanobacteria; Fluorescence Recovery Protein; Non-photochemical quenching; Orange Carotenoid Protein; Photoprotection; Phycobilisome;

Solution structure and excitation energy transfer in phycobiliproteins of Acaryochloris marina investigated by small angle scattering by M. Golub; S. Combet; D.C.F. Wieland; D. Soloviov; A. Kuklin; H. Lokstein; F.-J. Schmitt; R. Olliges; M. Hecht; H.-J. Eckert; J. Pieper (318-324).
The structure of phycobiliproteins of the cyanobacterium Acaryochloris marina was investigated in buffer solution at physiological temperatures, i.e. under the same conditions applied in spectroscopic experiments, using small angle neutron scattering. The scattering data of intact phycobiliproteins in buffer solution containing phosphate can be well described using a cylindrical shape with a length of about 225 Å and a diameter of approximately 100 Å. This finding is qualitatively consistent with earlier electron microscopy studies reporting a rod-like shape of the phycobiliproteins with a length of about 250 (M. Chen et al., FEBS Letters 583, 2009, 2535) or 300 Å (J. Marquart et al., FEBS Letters 410, 1997, 428). In contrast, phycobiliproteins dissolved in buffer lacking phosphate revealed a splitting of the rods into cylindrical subunits with a height of 28 Å only, but also a pronounced sample aggregation. Complementary small angle neutron and X-ray scattering experiments on phycocyanin suggest that the cylindrical subunits may represent either trimeric phycocyanin or trimeric allophycocyanin. Our findings are in agreement with the assumption that a phycobiliprotein rod with a total height of about 225 Å can accommodate seven trimeric phycocyanin subunits and one trimeric allophycocyanin subunit, each of which having a height of about 28 Å. The structural information obtained by small angle neutron and X-ray scattering can be used to interpret variations in the low-energy region of the 4.5 K absorption spectra of phycobiliproteins dissolved in buffer solutions containing and lacking phosphate, respectively.Display Omitted
Keywords: Acaryochloris marina; Phycobiliproteins; Excitation energy transfer; Small angle neutron scattering; Small angle X-ray scattering;

Structural insights into the cold adaptation of the photosynthetic pigment-protein C-phycocyanin from an Arctic cyanobacterium by Hai-Nan Su; Qian-Min Wang; Chun-Yang Li; Kang Li; Wei Luo; Bo Chen; Xi-Ying Zhang; Qi-Long Qin; Bai-Cheng Zhou; Xiu-Lan Chen; Yu-Zhong Zhang; Bin-Bin Xie (325-335).
The cold adaptation mechanism of phycobiliproteins, the major photosynthetic pigment-proteins in cyanobacteria and red algae, has rarely been studied. Here we reported the biochemical, structural, and molecular dynamics simulation study of the C-phycocyanin from Arctic cyanobacterial strain Pseudanabaena sp. LW0831. We characterized the phycobilisome components of LW0831 and obtained their gene sequences. Compared to the mesophilic counterpart from Arthrospira platensis (Ar-C-PC), LW0831 C-phycocyanin (Ps-C-PC) has a decreased thermostability (∆  T m of − 16 °C), one of the typical features of cold-adapted enzymes. To uncover its structural basis, we resolved the crystal structure of Ps-C-PC 1 at 2.04 Å. Consistent with the decrease in thermostability, comparative structural analyses revealed decreased intra-trimer and inter-trimer interactions in Ps-C-PC 1, compared to Ar-C-PC. However, comparative molecular dynamics simulations indicated that Ps-C-PC 1 shows similar flexibilities to Ar-C-PC for both the (αβ)3 trimer and (αβ)6 hexamer. Therefore, the optimization mode is clearly different from cold-adapted enzymes, which usually have increased flexibilities. Detailed analyses demonstrated different optimization modes for the α and β subunits and it was revealed that hydrophobic interactions are key to this difference, though salt bridges, hydrogen bonds, and surface hydrophobicity are also involved. This study is the first report of the structure of cold-adapted phycobiliproteins and provides insights into the cold-adaptation strategies of non-enzyme proteins.
Keywords: Algae; Photosynthesis; Phycobiliprotein; Crystallization; Stability; Flexibility;