Photosynthesis Research (v.106, #1-2)

Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation by Arthur R. Grossman; Steven J. Karpowicz; Mark Heinnickel; David Dewez; Blaise Hamel; Rachel Dent; Krishna K. Niyogi; Xenie Johnson; Jean Alric; Francis-André Wollman; Huiying Li; Sabeeha S. Merchant (3-17).
Chlamydomonas reinhardtii, a unicellular green alga, has been exploited as a reference organism for identifying proteins and activities associated with the photosynthetic apparatus and the functioning of chloroplasts. Recently, the full genome sequence of Chlamydomonas was generated and a set of gene models, representing all genes on the genome, was developed. Using these gene models, and gene models developed for the genomes of other organisms, a phylogenomic, comparative analysis was performed to identify proteins encoded on the Chlamydomonas genome which were likely involved in chloroplast functions (or specifically associated with the green algal lineage); this set of proteins has been designated the GreenCut. Further analyses of those GreenCut proteins with uncharacterized functions and the generation of mutant strains aberrant for these proteins are beginning to unmask new layers of functionality/regulation that are integrated into the workings of the photosynthetic apparatus.
Keywords: Chlamydomonas; GreenCut; Chloroplast; Phylogenomics; Regulation

Auxiliary electron transport pathways in chloroplasts of microalgae by Gilles Peltier; Dimitri Tolleter; Emmanuelle Billon; Laurent Cournac (19-31).
Microalgae are photosynthetic organisms which cover an extraordinary phylogenic diversity and have colonized extremely diverse habitats. Adaptation to contrasted environments in terms of light and nutrient’s availabilities has been possible through a high flexibility of the photosynthetic machinery. Indeed, optimal functioning of photosynthesis in changing environments requires a fine tuning between the conversion of light energy by photosystems and its use by metabolic reaction, a particularly important parameter being the balance between phosphorylating (ATP) and reducing (NADPH) power supplies. In addition to the main route of electrons operating during oxygenic photosynthesis, called linear electron flow or Z scheme, auxiliary routes of electron transfer in interaction with the main pathway have been described. These reactions which include non-photochemical reduction of intersystem electron carriers, cyclic electron flow around PSI, oxidation by molecular O2 of the PQ pool or of the PSI electron acceptors, participate in the flexibility of photosynthesis by avoiding over-reduction of electron carriers and modulating the NADPH/ATP ratio depending on the metabolic demand. Forward or reverse genetic approaches performed in model organisms such as Arabidopsis thaliana for higher plants, Chlamydomonas reinhardtii for green algae and Synechocystis for cyanobacteria allowed identifying molecular components involved in these auxiliary electron transport pathways, including Ndh-1, Ndh-2, PGR5, PGRL1, PTOX and flavodiiron proteins. In this article, we discuss the diversity of auxiliary routes of electron transport in microalgae, with particular focus in the presence of these components in the microalgal genomes recently sequenced. We discuss how these auxiliary mechanisms of electron transport may have contributed to the adaptation of microalgal photosynthesis to diverse and changing environments.
Keywords: ATP supply; Chlororespiration; Cyclic electron flow; Flavodiiron; PGR5; PGRL1; Photosynthesis; Plastid terminal oxidase; Redox poise

State transitions at the crossroad of thylakoid signalling pathways by Sylvain Lemeille; Jean-David Rochaix (33-46).
In order to maintain optimal photosynthetic activity under a changing light environment, plants and algae need to balance the absorbed light excitation energy between photosystem I and photosystem II through processes called state transitions. Variable light conditions lead to changes in the redox state of the plastoquinone pool which are sensed by a protein kinase closely associated with the cytochrome b 6 f complex. Preferential excitation of photosystem II leads to the activation of the kinase which phosphorylates the light-harvesting system (LHCII), a process which is subsequently followed by the release of LHCII from photosystem II and its migration to photosystem I. The process is reversible as dephosphorylation of LHCII on preferential excitation of photosystem I is followed by the return of LHCII to photosystem II. State transitions involve a considerable remodelling of the thylakoid membranes, and in the case of Chlamydomonas, they allow the cells to switch between linear and cyclic electron flow. In this alga, a major function of state transitions is to adjust the ATP level to cellular demands. Recent studies have identified the thylakoid protein kinase Stt7/STN7 as a key component of the signalling pathways of state transitions and long-term acclimation of the photosynthetic apparatus. In this article, we present a review on recent developments in the area of state transitions.
Keywords: Photosynthesis; State transitions; LHCII kinase; Arabidopsis; Chlamydomonas

Cyclic electron flow around PSI, or cyclic photophosphorylation, is the photosynthetic process which recycles the reducing equivalents produced by photosystem I in the stroma towards the plastoquinone pool. Through the activity of cytochrome b 6 f, which also transfers protons across the membrane, it promotes the synthesis of ATP. The literature dealing with cyclic electron flow in unicellular algae is far less abundant than it is for plants. However, in the chloroplast of algae such as Chlorella or Chlamydomonas, an efficient carbohydrate catabolism renders the redox poise much more reducing than in plant chloroplasts. It is therefore worthwhile highlighting the specific properties of unicellular algae because cyclic electron flow is highly dependent upon the accumulation of these stromal reducing equivalents. Such an increase of reducing power in the stroma stimulates the reduction of plastoquinones, which is the limiting step of cyclic electron flow. In anaerobic conditions in the dark, this reaction can lead to a fully reduced plastoquinone pool and induce state transitions, the migration of 80% of light harvesting complexes II and 20% of cytochrome b 6 f complex from the PSII-enriched grana to the PSI-enriched lamella. These ultrastructural changes have been proposed to further enhance cyclic electron flow by increasing PSI antenna size, and forming PSI-cyt b 6 f supercomplexes. These hypotheses are discussed in light of recently published data.
Keywords: Electron transfer; Green algae; Chlamydomonas reinhardtii ; Photosystem I; Cytochrome b 6 f

Eukaryotes acquired photosynthetic metabolism over a billion years ago, and during that time the light-harvesting antennae have undergone significant structural and functional divergence. The antenna systems are generally used to harvest and transfer excitation energy into the reaction centers to drive photosynthesis, but also have the dual role of energy dissipation. Phycobilisomes formed the first antenna system in oxygenic photoautotrophs, and this soluble protein complex continues to be the dominant antenna in extant cyanobacteria, glaucophytes, and red algae. However, phycobilisomes were lost multiple times during eukaryotic evolution in favor of a thylakoid membrane-integral light-harvesting complex (LHC) antenna system found in the majority of eukaryotic taxa. While photosynthesis spread across different eukaryotic kingdoms via endosymbiosis, the antenna systems underwent extensive modification as photosynthetic groups optimized their light-harvesting capacity and ability to acclimate to changing environmental conditions. This review discusses the different classes of LHCs within photosynthetic eukaryotes and examines LHC diversification in different groups in a structural and functional context.
Keywords: Light-harvesting complexes; Evolution; Antenna; Light-harvesting-like

The supramolecular architecture, function, and regulation of thylakoid membranes in red algae: an overview by Hai-Nan Su; Bin-Bin Xie; Xi-Ying Zhang; Bai-Cheng Zhou; Yu-Zhong Zhang (73-87).
Red algae are a group of eukaryotic photosynthetic organisms. Phycobilisomes (PBSs), which are composed of various types of phycobiliproteins and linker polypeptides, are the main light-harvesting antennae in red algae, as in cyanobacteria. Two morphological types of PBSs, hemispherical- and hemidiscoidal-shaped, are found in different red algae species. PBSs harvest solar energy and efficiently transfer it to photosystem II (PS II) and finally to photosystem I (PS I). The PS I of red algae uses light-harvesting complex of PS I (LHC I) as a light-harvesting antennae, which is phylogenetically related to the LHC I found in higher plants. PBSs, PS II, and PS I are all distributed throughout the entire thylakoid membrane, a pattern that is different from the one found in higher plants. Photosynthesis processes, especially those of the light reactions, are carried out by the supramolecular complexes located in/on the thylakoid membranes. Here, the supramolecular architecture, function and regulation of thylakoid membranes in red algal are reviewed.
Keywords: Red algae; Supramolecular complexes; Phycobilisome; Thylakoid membrane; Photosystem; Regulation

Carotenoid biosynthesis in diatoms by Martine Bertrand (89-102).
Diatoms are ubiquitous and constitute an important group of the phytoplankton community having a major contribution to the total marine primary production. These microalgae exhibit a characteristic golden-brown colour due to a high amount of the xanthophyll fucoxanthin that plays a major role in the light-harvesting complex of photosystems. In the water column, diatoms are exposed to light intensities that vary quickly from lower to higher values. Xanthophyll cycles prevent photodestruction of the cells in excessive light intensities. In diatoms, the diadinoxanthin–diatoxanthin cycle is the most important short-term photoprotective mechanism. If the biosynthetic pathways of chloroplast pigments have been extensively studied in higher plants and green algae, the research on carotenoid biosynthesis in diatoms is still in its infancy. In this study, the data on the biosynthetic pathway of diatom carotenoids are reviewed. The early steps occur through the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. Then a hypothetical pathway is suggested from dimethylallyl diphosphate (DMAPP) and isopentenyl pyrophosphate (IPP). Most of the enzymes of the pathway have not been so far isolated from diatoms, but candidate genes for each of them were identified using protein similarity searches of genomic data.
Keywords: Carotenoids; Diadinoxanthin; Diatoms; Diatoxanthin; MEP pathway; Xanthophylls

The xanthophyll cycle represents one of the important photoprotection mechanisms in plant cells. In the present review, we summarize current knowledge about the violaxanthin cycle of vascular plants, green and brown algae, and the diadinoxanthin cycle of the algal classes Bacillariophyceae, Xanthophyceae, Haptophyceae, and Dinophyceae. We address the biochemistry of the xanthophyll cycle enzymes with a special focus on protein structure, co-substrate requirements and regulation of enzyme activity. We present recent ideas regarding the structural basis of xanthophyll cycle-dependent photoprotection, including different models for the mechanism of non-photochemical quenching of chlorophyll a fluorescence. In a dedicated chapter, we also describe the unique violaxanthin antheraxanthin cycle of the Prasinophyceae, together with its implication for the mechanism of xanthophyll cycle-dependent heat dissipation. The interaction between the diadinoxanthin cycle and alternative electron flow pathways in the chloroplasts of diatoms is an additional topic of this review, and in the last chapter we cover aspects of the importance of xanthophyll cycle-dependent photoprotection for different algal species in their natural environments.
Keywords: Algae; Chlororespiration; NPQ; Photoprotection; Xanthophyll cycle

The phylogenetically and morphologically diverse eukaryotic algae are typically oxygenic photolithotrophs. They have a diversity of incompletely understood mechanisms of inorganic carbon acquisition: this article reviews four areas where investigations continue. The first topic is diffusive CO2 entry. Most eukaryotic algae, like all cyanobacteria, have inorganic carbon concentrating mechanisms (CCMs). The ancestral condition was presumably the absence of a CCM, i.e. diffusive CO2 entry, as found in a small minority of eukaryotic algae today; however, it is likely that, as is found in several cases, this condition is due to a loss of a CCM. There are a number of algae which are in various respects intermediate between diffusive CO2 entry and occurrence of a CCM: further study is needed on this aspect. A second topic is the nature of cyanelles and their role in inorganic carbon assimilation. The cyanelles (plastids) of the euglyphid amoeba Paulinella have been acquired relatively recently by endosymbiosis with genetic integration of an α-cyanobacterium with a Form 1A Rubisco. The α-carboxysomes in the cyanelles are presumably involved in a CCM, but further investigation is needed.Also called cyanelles are the plastids of glaucocystophycean algae, but is it now clear that these were derived from the β-cyanobacterial ancestor of all plastids other than that of Paulinella. The resemblances of the central body of the cyanelles of glaucocystophycean algae to carboxysomes may not reflect derivation from cyanobacterial β-carboxysomes; although it is clear that these algae have CCMs but these are now well characterized. The other two topics concern CCMs in other eukaryotic algae; these CCMs arose polyphyletically and independently of the cyanobacterial CCMs. It is generally believed that eukaryotic algal, like cyanobacterial, CCMs are based on active transport of an inorganic carbon species and/or protons, and they have C3 biochemistry. This is the case for the organism considered as the third topic, i.e. Chlamydomonas reinhardtii, the eukaryotic alga with the best understood CCM. This CCM involves HCO3 conversion to CO2 in the thylakoid lumen so the external inorganic carbon must cross four membranes in series with a final CO2 effux from the thylakoid. More remains to be investigated about this CCM. The final topic is that of the occurrence of C4-like metabolism in the CCMs of marine diatoms. Different conclusions have been reached depending on the organism investigated and the techniques used, and several aspects require further study.
Keywords: Bicarbonate; Carbon Dioxide; C3 biochemistry; C4 biochemistry; Diffusion; Genetic integration; Inorganic carbon concentrating mechanisms (CCMs)

The maximum quantum yield (Φ max), calculated from the maximum chlorophyll a specific photosynthetic rate divided by the quantum absorption per unit chlorophyll a, is 8 photons or 0.125 mol C per mol Quanta light energy. For the average solar radiation that reaches the earth’s surface this relates to a photosynthetic yield of 1.79 g(dw) m−2 day−1 per percentage photosynthetic efficiency and it could be doubled for sunny, dry and hot areas. Many factors determine volumetric yields of mass algal cultures and it is not simply a question of extrapolating controlled laboratory rates to large scale outdoor production systems. This is an obvious mistake many algal biotechnology start-up companies make. Closed photobioreactors should be able to outperform open raceway pond cultures because of the synergistic enhancement of a reduced boundary layer and short light/dark fluctuations at high turbulences. However, this has not been shown on any large scale and to date the industrial norm for very large production systems is open raceway production ponds. Microalgal biomass production offers real opportunities for addressing issues such as CO2 sequestration, biofuel production and wastewater treatment, and it should be the preferred research emphasis.
Keywords: Mass microalgal cultures; Quantum efficiency; Photobioreactor; Light fluctuations; Biofuels

The metabolic flexibility of some photosynthetic microalgae enables them to survive periods of anaerobiosis in the light by developing a particular photofermentative metabolism. The latter entails compounds of the photosynthetic electron transfer chain and an oxygen-sensitive hydrogenase in order to reoxidize reducing equivalents and to generate ATP for maintaining basal metabolic function. This pathway results in the photo-evolution of hydrogen gas by the algae. A decade ago, Melis and coworkers managed to reproduce such a condition in a laboratory context by depletion of sulfur in the algal culture media, making the photo-evolution by the algae sustainable for several days (Melis et al. in Plant Physiol 122:127–136, 2000). This observation boosted research in algal H2 evolution. A feature, which due to its transient nature was long time considered as a curiosity of algal photosynthesis suddenly became a phenomenon with biotechnological potential. Although the Melis procedure has not been developed into a biotechnological process of renewable H2 generation so far, it has been a useful tool for studying microalgal metabolic and photosynthetic flexibility and a possible step stone for future H2 production procedures. Ten years later most of the critical steps and limitations of H2 production by this protocol have been studied from different angles particularly with the model organism Chlamydomonas reinhardtii, by introducing various changes in culture conditions and making use of mutants issued from different screens or by reverse genomic approaches. A synthesis of these observations with the most important conclusions driven from recent studies will be presented in this review.
Keywords: Chlamydomonas reinhardtii ; Hydrogen evolution; Sulfur deficiency

Under stressful environments, many green algae such as Haematococcus pluvialis accumulate secondary ketocarotenoids such as canthaxanthin and astaxanthin. The carotenogenesis, responsible for natural phenomena such as red snows, generally accompanies larger metabolic changes as well as morphological modifications, i.e., the conversion of the green flagellated macrozoids into large red cysts. Astaxanthin accumulation constitutes a convenient way to store energy and carbon, which will be used for further synthesis under less stressful conditions. Besides this, the presence of high amount of astaxanthin enhances the cell resistance to oxidative stress generated by unfavorable environmental conditions including excess light, UV-B irradiation, and nutrition stress and, therefore, confers a higher survival capacity to the cells. This better resistance results from the quenching of oxygen atoms for the synthesis itself as well as from the antioxidant properties of the astaxanthin molecules. Therefore, astaxanthin synthesis corresponds to a multifunctional response to stress. In this contribution, the various biochemical, genetic, and molecular data related to the biosynthesis of ketocarotenoids by Haematococcus pluvialis and other taxa are reviewed and compared. A tentative regulatory model of the biochemical network driving astaxanthin production is proposed.
Keywords: Astaxanthin; Cytochrome P450 hydroxylase; Encystment; Haematococcus pluvialis ; Stress

Electrochromism: a useful probe to study algal photosynthesis by Benjamin Bailleul; Pierre Cardol; Cécile Breyton; Giovanni Finazzi (179-189).
In photosynthesis, electron transfer along the photosynthetic chain results in a vectorial transfer of protons from the stroma to the lumenal space of the thylakoids. This promotes the generation of an electrochemical proton gradient (Δμ H + ), which comprises a gradient of electric potential (ΔΨ) and of proton concentration (ΔpH). The Δμ H + has a central role in the photosynthetic process, providing the energy source for ATP synthesis. It is also involved in many regulatory mechanisms. The ΔpH modulates the rate of electron transfer and triggers deexcitation of excess energy within the light harvesting complexes. The ΔΨ is required for metabolite and protein transport across the membranes. Its presence also induces a shift in the absorption spectra of some photosynthetic pigments, resulting in the so-called ElectroChromic Shift (ECS). In this review, we discuss the characteristic features of the ECS, and illustrate possible applications for the study of photosynthetic processes in vivo.
Keywords: Spectroscopy; Electrochromism; Photosynthesis; Electrochemical proton gradient; ATP