Mössbauer studies of the non-heme iron and cytochrome b559 in a Chlamydomonas reinhardtii PSI- mutant and their interactions with alpha-tocopherol quinone

Unraveling the Mechanisms of Efficient Phosphorus Utilization in Popcorn (Zea mays L. var. everta): Insights from Proteomic and Metabolite Analysis

The expansion of agriculture and the need for sustainable practices drives breeders to develop plant varieties better adapted to abiotic stress such as nutrient deficiency, which negatively impacts yields. Phosphorus (P) is crucial for photosynthesis and plant growth, but its availability in the soil is often limited, hampering crop development. In this study, we examined the response of two popcorn inbred lines, L80 and P7, which have been characterized previously as P-use inefficient and P-use efficient, respectively, under low (stress) and high P (control) availability. Physiological measurements, proteomic analysis, and metabolite assays were performed to unravel the physiological and molecular responses associated with the efficient use of P in popcorn. We observed significant differences in protein abundances in response to the P supply between the two inbred lines. A total of 421 differentially expressed proteins (DEPs) were observed in L80 and 436 DEPs in P7. These proteins were involved in photosynthesis, protein biosynthesis, biosynthesis of secondary metabolites, and energy metabolism. In addition, flavonoids accumulated in higher abundance in P7. Our results help us understand the major components of P utilization in popcorn, providing new insights for popcorn molecular breeding programs.

Data-Independent-Acquisition-Based Proteomic Approach towards Understanding the Acclimation Strategy of Oleaginous Microalga Microchloropsis gaditana CCMP526 in Hypersaline Conditions

Salinity is one of the significant factors that affect growth and cellular metabolism, including photosynthesis and lipid accumulation, in microalgae and higher plants. Microchloropsis gaditana CCMP526 can acclimatize to different salinity levels by accumulating compatible solutes, carbohydrates, and lipids as energy storage molecules. We used proteomics to understand the molecular basis for acclimation of M. gaditana to increased salinity levels [55 and 100 PSU (practical salinity unit)]. Correspondence analysis was used for the identification of salinity-responsive proteins (SRPs). The highest number of salinity-induced proteins was observed in 100 PSU. Gene ontology enrichment analysis revealed a separate path of acclimation for cells exposed to 55 and 100 PSU. Osmolyte and lipid biosynthesis were upregulated in hypersaline conditions. Concomitantly, lipid oxidation pathways were also upregulated in hypersaline conditions, providing acetyl-CoA for energy metabolism through the tricarboxylic acid cycle. Carbon fixation and photosynthesis were tightly regulated, while chlorophyll biosynthesis was affected in hypersaline conditions. Importantly, temporal proteome analysis of salinity-induced M. gaditana revealed vital SRPs which could be used for engineering salinity resilient microalgal strains for improved productivity in hypersaline culture conditions.

Singlet oxygen oxidation products of carotenoids, fatty acids and phenolic prenyllipids

Singlet oxygen (¹O₂) is the major reactive oxygen species ROS causing photooxidative stress in plants which is formed predominantly in the reaction center of photosystem II during photosynthesis. To avoid deleterious effects of ¹O₂ oxygen on photosynthetic membrane components, plant synthesize a variety of ¹O₂ quenchers of lipophilic character, such as carotenoids or phenolic prenyllipids (tocopherols, plastochromanol-8, plastoquinol). In the process of chemical quenching of ¹O₂ by the antioxidants, both short-lived products, such as oxidized carotenoids, or relative long-lived compounds, such as oxidized phenolic prenyllipids are formed. The other target of ¹O₂ are unsaturated fatty acids of membrane lipids that undergo peroxidation as a result of the reaction. Some of the ¹O₂ oxidation products, like β-cyclocitral can be components of ¹O₂-signallingsignaling pathway leading to acclimatory responses of plants, while some others further fulfill antioxidant functions, like hydroxy-plastochromanol or hydroxy-plastoquinol. As most of the ¹O₂ oxidation products are specific compounds formed only as a results of ¹O₂ action, they can be very useful, specific molecular markers of ¹O₂-dependent oxidative stress in vivo.

Chloroplasts preferentially take up ferric-citrate over iron-nicotianamine complexes in Brassica napus

Fe uptake machinery of chloroplasts prefers to utilise Fe(III)-citrate over Fe-nicotianamine complexes. Iron uptake in chloroplasts is a process of prime importance. Although a few members of their iron transport machinery were identified, the substrate preference of the system is still unknown. Intact chloroplasts of oilseed rape (Brassica napus) were purified and subjected to iron uptake studies using natural and artificial iron complexes. Fe-nicotianamine (NA) complexes were characterised by 5 K, 5 T Mössbauer spectrometry. Expression of components of the chloroplast Fe uptake machinery was also studied. Fe(III)-NA contained a minor paramagnetic Fe(II) component (ca. 9%), a paramagnetic Fe(III) component exhibiting dimeric or oligomeric structure (ca. 20%), and a Fe(III) complex, likely being a monomeric structure, which undergoes slow electronic relaxation at 5 K (ca. 61%). Fe(II)-NA contained more than one similar chemical Fe(II) environment with no sign of Fe(III) components. Chloroplasts preferred Fe(III)-citrate compared to Fe(III)-NA and Fe(II)-NA, but also to Fe(III)-EDTA and Fe(III)-o,o'EDDHA, and the K_m value was lower for Fe(III)-citrate than for the Fe-NA complexes. Only the uptake of Fe(III)-citrate was light-dependent. Regarding the components of the chloroplast Fe uptake system, only genes of the reduction-based Fe uptake system showed high expression. Chloroplasts more effectively utilize Fe(III)-citrate, but hardly Fe-NA complexes in Fe uptake.

Gene essentiality, conservation index and co-evolution of genes in cyanobacteria

Cyanobacteria, a group of photosynthetic prokaryotes, dominate the earth with ~ 1015 g wet biomass. Despite diversity in habitats and an ancient origin, cyanobacterial phylum has retained a significant core genome. Cyanobacteria are being explored for direct conversion of solar energy and carbon dioxide into biofuels. For this, efficient cyanobacterial strains will need to be designed via metabolic engineering. This will require identification of target knockouts to channelize the flow of carbon toward the product of interest while minimizing deletions of essential genes. We propose "Gene Conservation Index" (GCI) as a quick measure to predict gene essentiality in cyanobacteria. GCI is based on phylogenetic profile of a gene constructed with a reduced dataset of cyanobacterial genomes. GCI is the percentage of organism clusters in which the query gene is present in the reduced dataset. Of the 750 genes deemed to be essential in the experimental study on S. elongatus PCC 7942, we found 494 to be conserved across the phylum which largely comprise of the essential metabolic pathways. On the contrary, the conserved but non-essential genes broadly comprise of genes required under stress conditions. Exceptions to this rule include genes such as the glycogen synthesis and degradation enzymes, deoxyribose-phosphate aldolase (DERA), glucose-6-phosphate 1-dehydrogenase (zwf) and fructose-1,6-bisphosphatase class1, which are conserved but non-essential. While the essential genes are to be avoided during gene knockout studies as potentially lethal deletions, the non-essential but conserved set of genes could be interesting targets for metabolic engineering. Further, we identify clusters of co-evolving genes (CCG), which provide insights that may be useful in annotation. Principal component analysis (PCA) plots of the CCGs are demonstrated as data visualization tools that are complementary to the conventional heatmaps. Our dataset consists of phylogenetic profiles for 23,643 non-redundant cyanobacterial genes. We believe that the data and the analysis presented here will be a great resource to the scientific community interested in cyanobacteria.

Molecular Mechanisms behind the Physiological Resistance to Intense Transient Warming in an Iconic Marine Plant

The endemic Mediterranean seagrass Posidonia oceanica is highly threatened by the increased frequency and intensity of heatwaves. Meadows of the species offer a unique opportunity to unravel mechanisms marine plants activate to cope transient warming, since their wide depth distribution impose divergent heat-tolerance. Understanding these mechanisms is imperative for their conservation. Shallow and deep genotypes within the same population were exposed to a simulated heatwave in mesocosms, to analyze their transcriptomic and photo-physiological responses during and after the exposure. Shallow plants, living in a more unstable thermal environment, optimized phenotype variation in response to warming. These plants showed a pre-adaptation of genes in anticipation of stress. Shallow plants also showed a stronger activation of heat-responsive genes and the exclusive activation of genes involved in epigenetic mechanisms and in molecular mechanisms that are behind their higher photosynthetic stability and respiratory acclimation. Deep plants experienced higher heat-induced damage and activated metabolic processes for obtaining extra energy from sugars and amino acids, likely to support the higher protein turnover induced by heat. In this study we identify transcriptomic mechanisms that may facilitate persistence of seagrasses to anomalous warming events and we discovered that P. oceanica plants from above and below the mean depth of the summer thermocline have differential resilience to heat.

Salinity-Induced Palmella Formation Mechanism in Halotolerant Algae Dunaliella salina Revealed by Quantitative Proteomics and Phosphoproteomics

Palmella stage is critical for some unicellular algae to survive in extreme environments. The halotolerant algae Dunaliella salina is a good single-cell model for studying plant adaptation to high salinity. To investigate the molecular adaptation mechanism in salinity shock-induced palmella formation, we performed a comprehensive physiological, proteomics and phosphoproteomics study upon palmella formation of D. salina using dimethyl labeling and Ti⁴⁺-immobilized metal ion affinity chromatography (IMAC) proteomic approaches. We found that 151 salinity-responsive proteins and 35 salinity-responsive phosphoproteins were involved in multiple signaling and metabolic pathways upon palmella formation. Taken together with photosynthetic parameters and enzyme activity analyses, the patterns of protein accumulation and phosphorylation level exhibited the mechanisms upon palmella formation, including dynamics of cytoskeleton and cell membrane curvature, accumulation and transport of exopolysaccharides, photosynthesis and energy supplying (i.e., photosystem II stability and activity, cyclic electron transport, and C4 pathway), nuclear/chloroplastic gene expression regulation and protein processing, reactive oxygen species homeostasis, and salt signaling transduction. The salinity-responsive protein-protein interaction (PPI) networks implied that signaling and protein synthesis and fate are crucial for modulation of these processes. Importantly, the 3D structure of phosphoprotein clearly indicated that the phosphorylation sites of eight proteins were localized in the region of function domain.

The dynamics of the non-heme iron in bacterial reaction centers from Rhodobacter sphaeroides

We investigate the dynamical properties of the non-heme iron (NHFe) in His-tagged photosynthetic bacterial reaction centers (RCs) isolated from Rhodobacter (Rb.) sphaeroides. Mössbauer spectroscopy and nuclear inelastic scattering of synchrotron radiation (NIS) were applied to monitor the arrangement and flexibility of the NHFe binding site. In His-tagged RCs, NHFe was stabilized only in a high spin ferrous state. Its hyperfine parameters (IS=1.06±0.01mm/s and QS=2.12±0.01mm/s), and Debye temperature (θ(D0)~167K) are comparable to those detected for the high spin state of NHFe in non-His-tagged RCs. For the first time, pure vibrational modes characteristic of NHFe in a high spin ferrous state are revealed. The vibrational density of states (DOS) shows some maxima between 22 and 33meV, 33 and 42meV, and 53 and 60meV and a very sharp one at 44.5meV. In addition, we observe a large contribution of vibrational modes at low energies. This iron atom is directly connected to the protein matrix via all its ligands, and it is therefore extremely sensitive to the collective motions of the RC protein core. A comparison of the DOS spectra of His-tagged and non-His-tagged RCs from Rb. sphaeroides shows that in the latter case the spectrum was overlapped by the vibrations of the heme iron of residual cytochrome c(2), and a low spin state of NHFe in addition to its high spin one. This enabled us to pin-point vibrations characteristic for the low spin state of NHFe.

Uptake and incorporation of iron in sugar beet chloroplasts

Chloroplasts contain 80-90% of iron taken up by plant cells. Though some iron transport-related envelope proteins were identified recently, the mechanism of iron uptake into chloroplasts remained unresolved. To shed more light on the process of chloroplast iron uptake, trials were performed with isolated intact chloroplasts of sugar beet (Beta vulgaris). Iron uptake was followed by measuring the iron content of chloroplasts in the form of ferrous-bathophenantroline-disulphonate complex after solubilising the chloroplasts in reducing environment. Ferric citrate was preferred to ferrous citrate as substrate for chloroplasts. Strong dependency of ferric citrate uptake on photosynthetic electron transport activity suggests that ferric chelate reductase uses NADPH, and is localised in the inner envelope membrane. The K(m) for iron uptake from ferric-citrate pool was 14.65 ± 3.13 μM Fe((III))-citrate. The relatively fast incorporation of (57)Fe isotope into Fe-S clusters/heme, detected by Mössbauer spectroscopy, showed the efficiency of the biosynthetic machinery of these cofactors in isolated chloroplasts. The negative correlation between the chloroplast iron concentration and the rate of iron uptake refers to a strong feedback regulation of the uptake.

Light-induced quinone reduction in photosystem II

The photosystem II core complex is the water:plastoquinone oxidoreductase of oxygenic photosynthesis situated in the thylakoid membrane of cyanobacteria, algae and plants. It catalyzes the light-induced transfer of electrons from water to plastoquinone accompanied by the net transport of protons from the cytoplasm (stroma) to the lumen, the production of molecular oxygen and the release of plastoquinol into the membrane phase. In this review, we outline our present knowledge about the "acceptor side" of the photosystem II core complex covering the reaction center with focus on the primary (Q(A)) and secondary (Q(B)) quinones situated around the non-heme iron with bound (bi)carbonate and a comparison with the reaction center of purple bacteria. Related topics addressed are quinone diffusion channels for plastoquinone/plastoquinol exchange, the newly discovered third quinone Q(C), the relevance of lipids, the interactions of quinones with the still enigmatic cytochrome b559 and the role of Q(A) in photoinhibition and photoprotection mechanisms. This article is part of a Special Issue entitled: Photosystem II.

Occurrence, biosynthesis and function of isoprenoid quinones

Isoprenoid quinones are one of the most important groups of compounds occurring in membranes of living organisms. These compounds are composed of a hydrophilic head group and an apolar isoprenoid side chain, giving the molecules a lipid-soluble character. Isoprenoid quinones function mainly as electron and proton carriers in photosynthetic and respiratory electron transport chains and these compounds show also additional functions, such as antioxidant function. Most of naturally occurring isoprenoid quinones belong to naphthoquinones or evolutionary younger benzoquinones. Among benzoquinones, the most widespread and important are ubiquinones and plastoquinones. Menaquinones, belonging to naphthoquinones, function in respiratory and photosynthetic electron transport chains of bacteria. Phylloquinone K(1), a phytyl naphthoquinone, functions in the photosynthetic electron transport in photosystem I. Ubiquinones participate in respiratory chains of eukaryotic mitochondria and some bacteria. Plastoquinones are components of photosynthetic electron transport chains of cyanobacteria and plant chloroplasts. Biosynthetic pathway of isoprenoid quinones has been described, as well as their additional, recently recognized, diverse functions in bacterial, plant and animal metabolism.

Tocopherol quinone content of green algae and higher plants revised by a new high-sensitive fluorescence detection method using HPLC--effects of high light stress and senescence

A rapid, sensitive fluorescence method was applied here for detection of oxidized tocopherol quinones in total plant tissue extracts using HPLC, employing a post-column reduction of these compounds by a Zn column. Using this method, we were able to detect both alpha- and gamma-tocopherol quinones in Chlamydomonas reinhardii with a very high degree of sensitivity. The levels of both compounds increased under high light stress in the presence of pyrazolate in parallel to a decrease in the content of the corresponding tocopherols. The formation of tocopherol quinones from tocopherols was apparently due to their oxidation by singlet oxygen, which is formed in photosystem II under high light stress. alpha-Tocopherol quinone was also detected in a variety of higher plants of different age, and its level was found to increase during senescence in leaves grown under natural conditions. In contrast to alpha-tocopherol quinone, gamma-tocopherol quinone was not found in the higher plant species investigated with the exception of young runner bean leaves, where the levels of both compounds increased dramatically during cold and light stress. Taking advantage of native fluorescence of the reduced alpha-tocopherol quinone (alpha-tocopherol quinol), it can be detected in plant tissue extracts with a high sensitivity. In young runner bean leaves, alpha-tocopherol quinol was found at a level similar to alpha-tocopherol.

Structure-property relationships in the crystals of the smallest amino acid: an incoherent inelastic neutron scattering study of the glycine polymorphs

Incoherent inelastic neutron scattering spectra for the three crystalline polymorphs (alpha- P2(1)/n, beta- P2(1), gamma- P3(1)) of glycine (C2H5NO2) at temperatures between 5 and 300 K (using the time-of-flight (ToF) spectrometer NEAT at HMI) and at pressures from ambient up to 1 GPa (using the ToF spectrometer IN6 at the ILL) were measured. Significant differences in the band positions and their relative intensities in the density of states (DoS) were observed for the three polymorphs, which can be related to the different intermolecular interactions. The mean-squared displacement, <u(2)>(T), dependence reveals a change in dynamic properties at about the same temperature (150 K) for all the three forms, which can be related to the reorientation of the NH3 group. Besides, a dynamic transition in beta-glycine at about 230-250 K on cooling was also observed, supporting previously obtained adiabatic calorimetry data. This behavior is similar to that already observed in amorphous solids, on approaching the glass transition temperatures, as well as in biological systems. It suggests the onset of degrees of freedom most likely related to transitions between slightly different conformational orientations. The DoS obtained as a function of pressure has confirmed the stability of the alpha-form with respect to pressure and also depicted a sign of the previously reported reversible beta-beta' glycine phase transition in between 0.6 and 0.8 GPa. Moreover, a remarkable kinetic effect in the pressure-induced phase transition in gamma-glycine was revealed. After the sample was kept at 0.8 GPa for an hour in the neutron beam, an irreversible transition into a high-pressure form (different from the beta'-form) occurred, although previously in X-Ray diffraction and Raman spectroscopy experiments a gamma- to delta-glycine phase transition was observed above 3.5 GPa only.

Plastoquinol as a singlet oxygen scavenger in photosystem II

It has been found that in Chlamydomonas reinhardtii cells, under high-light stress, the level of reduced plastoquinone considerably increases while in the presence of pyrazolate, an inhibitor of plastoquinone and tocopherol biosynthesis, the content of reduced plastoquinone quickly decreases, similarly to alpha-tocopherol. In relation to chlorophyll, after 18 h of growth under low light with the inhibitor, the content of alpha-tocopherol was 22.2 mol/1000 mol chlorophyll and that of total plastoquinone (oxidized and reduced) was 19 mol/1000 mol chlorophyll, while after 2 h of high-light stress the corresponding amounts dropped to 6.4 and 6.2 mol/1000 mol chlorophyll for alpha-tocopherol and total plastoquinone, respectively. The degradation of both prenyllipids was partially reversed by diphenylamine, a singlet oxygen scavenger. It was concluded that plastoquinol, as well as alpha-tocopherol is decomposed under high-light stress as a result of a scavenging reaction of singlet oxygen generated in photosystem II. The levels of both alpha-tocopherol and of the reduced plastoquinone are not affected significantly in the absence of the inhibitor due to a high turnover rate of both prenyllipids, i.e., their degradation is compensated by fast biosynthesis. The calculated turnover rates under high-light conditions were twofold higher for total plastoquinone (0.23 nmol/h/ml of cell culture) than for alpha-tocopherol (0.11 nmol/h/ml). We have also found that the level of alpha-tocopherolquinone, an oxidation product of alpha-tocopherol, increases as the alpha-tocopherol is consumed. The same correlation was also observed for gamma-tocopherol and its quinone form. Moreover, in the presence of pyrazolate under low-light growth conditions, the synthesis of plastoquinone-C, a hydroxylated plastoquinone derivative, was stimulated in contrast to plastoquinone, indicating for the first time a functional role for plastoquinone-C. The presented data also suggest that the two plastoquinones may have different biosynthetic pathways in C. reinhardtii.

Dynamics of electron transfer in photosystem II

Photosystem II, being a constituent of light driven photosynthetic apparatus, is a highly organized pigment-protein-lipid complex. The arrangement of PSII active redox cofactors insures efficiency of electron transfer within it. Donation of electrons extracted from water by the oxygen evolving complex to plastoquinones requires an additional activation energy. In this paper we present theoretical discussion of the anharmonic fluctuations of the protein-lipid matrix of PSII and an experimental evidence showing that the fluctuations are responsible for coupling of its donor and acceptor side. We argue that the fast collective motions liberated at temperatures higher that 200 K are crucial for the two final steps of the water splitting cycle and that one can distinguish three different dynamic regimes of PSII action which are controlled by the timescales of forward electron transfer, which vary with temperature. The three regimes of the dynamical behavior are related to different spatial domains of PSII.

Fluorescence Lifetimes Study of α-Tocopherol and Biological Prenylquinols in Organic Solvents and Model Membranes

We have found that for biological prenyllipids, such as plastoquinol-9, alpha-tocopherol quinol, and alpha-tocopherol, the shortest fluorescence lifetimes were found in aprotic solvents (hexane, ethyl acetate) whereas the longest lifetimes were those of ubiquinonol-10 in these solvents. For all the investigated prenyllipids, fluorescence lifetime in alcohols increased along with an increase in solvent viscosity. In a concentrated hexane solution, the lifetimes of prenylquinols considerably decreased. This contrasts with methanol solutions, which is probably due to the self-association of these compounds in aprotic solvents. We have also found a correlation of the Stokes shift of prenyllipids fluorescence with the orientation polarizability of the solvents. Based on data obtained in organic solvents, measurements of the fluorescence lifetimes of prenyllipids in liposomes allowed an estimation of the relative distance of their fluorescent rings from the liposome membrane surface, and was found to be the shortest for alpha-tocopherol quinol in egg yolk phosphatidylcholine liposomes, and increased in the following order: alpha-tocopherol in dipalmitoyl phosphatidylcholine liposomes < alpha-tocopherol < plastoquinol-9 < ubiquinol-10 in egg-yolk phosphatidylcholine liposomes.

Tocopherol as singlet oxygen scavenger in photosystem II

Singlet oxygen is formed in the photosystem II reaction center in the quench of P680 triplets, and the yield is dependent on light intensity and the reduction level of plastoquinone. Singlet oxygen in PS II triggers the degradation of the D1 protein. We investigated the participation of tocopherol as a singlet oxygen scavenger in this system. For this purpose, we inhibited tocopherol biosynthesis at the level of the HPP-dioxygenase in the alga Chlamydomonas reinhardtii under conditions in which plastoquinone did not limit the photosynthesis rate. In the presence of the inhibitor and in high light for 2 h, photosynthesis in vivo and photosystem II was inactivated, the D1 protein was degraded, and the tocopherol pool was depleted and fell below its turnover rate/h. The inhibited system could be fully resuscitated upon the addition of a chemical singlet oxygen quencher (diphenylamine), and partly by synthetic cell wall permeable short chain alpha- and gamma-tocopherol derivatives. We conclude that under conditions of photoinhibition and extensive D1 protein turnover tocopherol has a protective function as a singlet oxygen scavenger.