1. Chloroplast Lipids

Yonghong Zhou, Katharina vom Dorp, Peter Dörmann and Georg Hölzl

Chloroplasts are the major site of fatty acid de novo synthesis in the cells of plants and algae. Fatty acids are incorporated into glycerolipids in the chloroplast (prokaryotic pathway) or are exported to the endoplasmic reticulum for glycerolipid synthesis following the eukaryotic pathway. The four major glycerolipids of chloroplasts are monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), sulfoquinovosyldiacylglycerol (SQDG) and phosphatidylglycerol (PG), which are the building blocks for thylakoids and play specific roles in photosynthesis. During phosphate deprivation DGDG and SQDG accumulate and replace phospholipids to save phosphate for other processes. In addition to glycerolipids, chloroplasts contain a large variety of isoprenoid lipids derived from the methyl-erythritol-phosphate pathway. Prenylquinones (tocopherol, plastoquinone, phylloquinone) are one class of chloroplast isoprenoid lipids and serve as antioxidants or electron carriers of photosystems II and I, respectively. β-Carotene (an isoprenoid-derived carotenoid), tocopherol, and phylloquinone (provitamin A, vitamin E and vitamin K1, respectively) are essential components of the human diet. Chlorophyll, the main photosynthetic pigment, carries an isoprenoid-derived phytyl chain which is released during chlorophyll breakdown. Phytol is employed for the synthesis of fatty acid phytyl esters and tocopherol. In contrast to plants, chloroplasts of eukaryotic algae contain further lipids and employ additional routes for lipid synthesis. Research on chloroplast lipids has seen major progress in the recent past due to the development of highly sensitive and accurate mass spectrometers for the analysis of extremely low abundant lipids or lipids only accumulating during stress conditions.

2. Assembly and Degradation of Pigment-binding Proteins

Tania Tibiletti, Miguel A. Hernández-Prieto, Trudi A. Semeniuk and Christiane Funk

In organisms performing oxygenic photosynthesis, the light absorbed by the Photosystem II reaction center is used to power the extraction of electrons from water, and initiate a series of oxidation-reduction reactions that power the synthesis of energy-rich molecules (ATP and NAD(P)H). These energy-rich molecules are transported to other cellular compartments to power all the metabolic reactions required to maintain growth. To ensure a constant supply of energy and avoid deleterious reactions caused by the absorption of excess sun light, photosynthetic organisms have evolved different mechanisms to reduce or increase the number of pigment-binding molecules present in their thylakoids. This chapter offers a current overview of the processes underlying assembly, degradation, and repair of the pigment-binding complexes present in higher plants, green algae, and cyanobacteria. We focus specifically on the chlorophyll-binding complexes in these organisms.

3. Structural and Functional Dynamics of the Thylakoid Membrane System

Sujith Puthiyaveetil, Helmut Kirchhoff and Ricarda Höhner

The thylakoid membrane harbors the photosynthetic machinery and is the site of light reactions in plants, algae, and cyanobacteria. In plants and green algae it stacks up to form the remarkable granal structures, the origin of which is likely to be a compromise between efficient light harvesting and diffusional freedom of electron carriers. Diffusional limitation in the highly crowded thylakoid membrane may also keep the grana diameter in check. The semi-crystalline array formation of photosystems and compositional changes in thylakoid lipids are strategies to overcome diffusional limitations under a variety of abiotic stresses. Under light and nutrient stress, the thylakoid membrane is profoundly reconfigured in ultrastructure, organization and composition. This striking plasticity in the structure and function of the thylakoid membrane tunes photosynthetic energy conversion in changing environmental and developmental conditions. A complete understanding of thylakoid membrane flexibility may illuminate and inform reengineering of photosynthesis and the design of artificial photosynthetic membranes.

4. Distinct Energetics and Regulatory Functions of the Two Major Cyclic Electron Flow Pathways in Chloroplasts

Deserah D. Strand, Nicholas Fisher and David M. Kramer

The output of the light reactions of photosynthesis, i.e. ATP and NADPH, must be finely controlled to meet the varying metabolic demands of the plant. Deleterious side reactions, including the production of reactive oxygen species (ROS), can occur if this balance is not maintained. In this Chapter, we review recent advances in understanding of cyclic electron flow around photosystem I (CEF), a process that evolved to correct for such energy imbalances. CEF in higher plants has been proposed to function primarily through two pathways: the ferredoxin:plastoquinone reductase (FQR) and the NADPH dehydrogenase complex (NDH). Because these pathways appear to support the same function, they are often thought to be redundant. However, it was recently shown that the NDH complex is a type I proton pumping quinone reductase, making the complex a more efficient route for ATP generation via CEF than the FQR. In addition, these pathways are differentially regulated, the FQR through chloroplast redox status, and the NDH thermodynamically and, in part, by hydrogen peroxide. These observations imply that the two pathways are distinct in terms of their energetics and regulation and thus it is clear that the FQR and the NDH work under different conditions to provide with rapid or efficient energy balancing of the chloroplast. Specifically, we suggest a CEF model in which the FQR is rapidly activated to restore balance when an ATP deficit leads to a buildup of reducing power in the stroma, and the NDH activated when a prolonged deficit leads to closure of the PSI acceptor side with associated ROS production.

5. Modeling Electron and Proton Transport in Chloroplasts

Alexander N. Tikhonov

Mathematical modeling of photosynthesis provides a framework for in-depth analysis of light energy transduction and feedbacks in the network of plant cell metabolism. In this Chapter, mathematical models of oxygenic photosynthesis are considered in the context of light-induced regulation of photosynthetic electron and proton transport in chloroplasts, the energy transducing organelles of the plant cell. After a brief overview of electron and proton transport processes in chloroplasts and basic mechanisms of their regulation, general approaches to mathematical description of photosynthetic processes are outlined. As an example of computer modeling of oxygenic photosynthesis, a generalized mathematical model of electron and proton transport in chloroplasts is described. The model includes key stages of linear electron transport, alternative pathways of electron transfer around Photosystem I, transmembrane proton transport and ATP synthesis. The model also takes into account pH-dependent mechanisms of the intersystem electron transport control and the light-induced activation of the Calvin-Benson cycle. Some peculiarities of diffusion-controlled reactions of electron and proton transport in chloroplasts are described within the framework of the model which takes into account lateral heterogeneity of thylakoid membranes. At the end of the Chapter, future trends in modeling electron and proton transport in chloroplasts are analyzed.

6. New Players for Photoprotection and Light Acclimation

Denis Jallet, Michael Cantrell and Graham Peers

Light is the source of energy for oxygenic photosynthesis. Large variations in light availability expose photoautotrophic organisms to low fluxes that limit net photosynthesis and high fluxes that are in great excess of photosynthetic capacity. Plants, algae and cyanobacteria need to adjust their photosynthetic apparatus over the time scales of light variability - from seconds to seasons - to balance the energy needs of the organism and to avoid the photooxidative damage associated with excess light energy absorption (photoprotection). This chapter reviews recent discoveries regarding the light acclimation and photoprotective processes within the chloroplast and cyanobacteria. We focus on energy dissipation pathways and the signaling pathways associated with the response to excess light stress.

7. Photoinhibition and the Damage-Repair Cycle of Photosystem II

Yasusi Yamamoto and Miho Yoshioka-Nishimura

Excessive illumination of Photosystem II in oxygenic photosynthetic organisms, such as cyanobacteria, algae and higher plants, causes photoinhibition and blocks electron transport in Photosystem II. In this event, the reaction center D1 protein is damaged primarily by reactive oxygen species or other endogenous radicals produced by the photochemical reaction, and degradation and/or irreversible aggregation of the damaged proteins occur subsequently. When the D1 protein is photodamaged under moderate high light or weak light, the damaged protein is proteolyzed and replaced by a newly synthesized copy. The photoinhibition under these conditions is reversible and Photosystem II activity recovers rapidly in the dark. In contrast, irreversible aggregation of the D1 protein, which is caused by excessive illumination, prevents proper D1 turnover. Once the aggregated products accumulate in Photosystem II complexes their removal by proteases is hampered. The photoinhibition observed under these conditions is irreversible. In higher plant chloroplasts, illumination with high light leads to dynamic changes in the structure of the thylakoids at the molecular and membrane levels. It has become clear recently that these structural changes are necessary so that Photosystem II can endure the effects of light stress effectively.

8. Plastoglobules: Lipid Droplets at the Thylakoid Membrane

Thibaut Pralon and Felix Kessler

Plastoglobules (PG) are lipid droplets that are structurally and functionally associated with the thylakoid membranes of chloroplasts. PG thus effectively form a thylakoid membrane microdomain. The thylakoid membranes provide the environment for the photosynthetic light reactions. The thylakoid membranes in majority consist of bilayer forming galactolipids and also harbor neutral lipids, including carotenoids, chlorophylls, prenylquinones (plastoquinone, phylloquinone, tocopherols), and others. The neutral lipids participate directly in the photosynthetic light reactions, act as anti-oxidants or are metabolic products, respectively. The biosynthesis, abundance, redox state and other parameters of these compounds are tightly controlled. PG store these compounds but also actively participate in their metabolism. PG thereby contribute to continuous remodeling of the thylakoid membrane. This depends on the presence of an assortment of enzymes and regulatory kinases at PG that are involved in wide range of processes affecting thylakoid membrane composition. Here, we review the current state of the PG field.

9. Redox Regulation in Chloroplasts

Monica Balsera, Peter Schürmann and Bob B. Buchanan

The reversible oxidation of cysteine (Cys) residues is commonly used to regulate a range of cellular processes throughout biology. Modification of regulatory Cys alters protein solubility and activity and, under control conditions, ultimately results in the fine-tuning of processes in response to metabolic demands. In oxyphotosynthetic organisms, the reversible modification of protein thiols is a major mechanism for direct regulation of chloroplast enzymes in a light-dependent manner and in response to different types of stress. The main redox regulatory system in chloroplasts is the ferredoxin-dependent thioredoxin system (FTS) which coordinates metabolic pathways of oxygenic photosynthesis via thioredoxin-mediated dithiol/disulfide (SH/S-S) transitions. NADP-linked thioredoxin reductase C and the glutathione/glutaredoxin systems complement the FTS in maintaining redox balance under certain environmental conditions.

10. The Transporters of Plastids - New Insights into an Old Field

Karsten Fischer, Andreas P.M. Weber and Hans-Henning Kunz

Plastids are the hallmark organelles of all photosynthetic eukaryotes and are the site of major anabolic pathways. Metabolic pathways within chloroplasts are highly connected with pathways occurring in the surrounding cytosol and in other organelles, which mandates a massive flux of organic solutes across the chloroplast envelope membranes. In addition, inorganic ions, taken up by the roots and transported to the other plant organs, have to be distributed within the cell to the different organelles, including plastids. Hence, a plethora of metabolite and ion transport systems that mediate these fluxes are found in plastids. During the evolution of chloroplasts from a cyanobacterial ancestor, the majority of the chloroplast envelope membrane transporters were recruited from the pre-existing repertoire of host transporters whilst only few are of cyanobacterial provenance. We will review the current knowledge on chloroplast metabolite and ion transporters from an evolutionary perspective and for some discuss their physiological functions.

11. The GreenCut - Functions and Relationships of Proteins Conserved in Green Lineage Organisms

Tyler M. Wittkopp, Shai Saroussi, Wenqiang Yang and Arthur R. Grossman

The most recent GreenCut (GreenCut2) represents a collection of 597 proteins in Chlamydomonas and other green lineage photosynthetic organisms, but not in non-photosynthetic (heterotrophic) organisms. GreenCut2 proteins have diverse functions, with many involved in chloroplast processes including photosynthesis and various biosynthetic pathways. GreenCut2 proteins also have roles in assembly and maintenance of chloroplasts, as well as in plant and algal regulatory processes. This chapter focuses on how GreenCut2 bioinformatic analyses were performed, discusses new insights into GreenCut2 proteins that have recently been characterized, suggests new ways to group these proteins based on their known or inferred biological functions, and reexamines potential functions of some GreenCut2 'unknowns' for which there is now experimental information.