Plants and algae are subjected to changes in light quality and quantity and in nutrient availability in their natural habitat. To adapt to these changing environmental conditions, these organisms have developed efficient means to adjust their photosynthetic apparatus so as to preserve photosynthetic efficiency and appropriate photoprotection. Under limiting light, this system optimizes light capture and photosynthetic yield through a reorganization of its light-harvesting system. In contrast, under high light, when the absorption capacity of the system is exceeded, the excess absorbed light energy is dissipated as heat to prevent oxidative damage. One of the key photosynthetic complexes, photosystem II, is prone to photodamage but is efficiently repaired. The photosynthetic machinery is also able to adjust when specific micronutrients such as copper, iron or sulfur become limiting by remodeling some of the photosynthetic complexes and metabolic pathways. While some of these responses occur in the short term, others occur in the long term and involve an intricate signaling system within chloroplasts and between the chloroplast and the nucleus accompanied with changes in gene expression. These signals involve the tetrapyrrole pathway, plastid protein synthesis, the redox state of the photosynthetic electron transport chain, reactive oxygen species and several metabolites.
- thylakoid membrane
- retrograde signaling
Photosynthetic organisms are constantly subjected to changes in light quality and quantity and have to adapt to this changing environment. On the one hand they need light energy and have to collect it efficiently especially when light is limiting; on the other hand, they have to be able to dissipate the excess absorbed light energy when the capacity of the photosynthetic apparatus is exceeded. The primary events of photosynthesis occur in the thylakoids, a complex network of membranes localized within chloroplasts. These primary reactions are mediated by three major protein–pigment complexes, photosystem II (PSII), the cytochrome
Linear electron flow (LEF) and cyclic electron flow (CEF) are shown in red and blue, respectively, with arrows indicating the direction of electron flow. The LEF pathway is driven by the two photochemical reactions of PSII and PSI: electrons are extracted by PSII from water and transferred subsequently to the PQ pool, Cyt
A striking feature of the thylakoid membrane is its lateral heterogeneity with two distinct domains consisting of appressed membranes, called grana, and stromal lamellae, which connect the grana regions with each other [6,7]. Whereas PSII is mainly localized in the grana regions, PSI and the ATP synthase are found in the stromal lamellae and in the margins of the grana . This is because these two complexes have large domains protruding in the stromal phase which do not fit into the narrow membrane space between the grana lamellae. The organization of thylakoid membranes in the grana and stromal regions is determined to a large extent by the resident photosystem complexes. As an example, mutants deficient in PSI contain mostly grana with few stromal lamellae [9,10]. In contrast to the photosystems, the Cyt
The LHCII and LHCI genes form a large family with each member encoding a protein with three transmembrane domains and up to eight chlorophyll
The aim of this chapter is to provide a description of the remarkable dynamics and flexibility of the photosynthetic apparatus of algae in response to changes in environmental conditions and to compare these responses with those of land plants. They include changes in light quality and quantity and in nutrient availability. These responses involve a reorganization of some of the photosynthetic complexes often mediated by posttranslational modifications of their subunits through an extensive signaling network in chloroplasts and between chloroplasts and nucleus which modulates nuclear and plastid gene expression.
2. Adaptation to changes in light conditions
A distinctive feature of photosynthetic organisms is the presence of light-harvesting systems that funnel the absorbed light energy to the corresponding reaction centers and thereby considerably increase their absorption cross-section. Several regulatory mechanisms operate on these antenna systems for controlling the energy flux to the reaction centers. This is particularly important under changing environmental conditions when the photosynthetic apparatus needs to adapt quickly. Under limiting light, it optimizes its light absorption efficiency by adjusting the relative size of its antenna systems through the reversible allocation of a portion of LHCII between PSII and PSI, a process referred to as state transitions which occurs in algae, plants and cyanobacteria (for reviews see Refs. [17,18]). In contrast, when the absorbed light energy exceeds the capacity of the photosynthetic apparatus, it dissipates the excess excitation energy through nonphotochemical quenching (NPQ) as heat thereby avoiding photodamage (for reviews see Refs. [19,20]).
2.1. State transitions
Because the antenna systems of PSII and PSI have a different pigment composition, their relative light absorption properties change when the light quality varies. This is especially important for aquatic algae because the penetration of light in water changes depending on its wavelength; in particular, red light is more absorbed than blue light. Another example is provided by photosynthetic organisms growing under a canopy where far red light is enriched. These changes in light quality can result in an unequal excitation of PSII and PSI and thereby perturb the redox poise of the plastoquinone pool. Over excitation of PSII relative to PSI leads to increased reduction of the plastoquinone pool and favors thereby docking of plastoquinol to the Qo site of the Cyt
State transitions do not occur under high light because the LHCII kinase is inactivated . The current view is that inactivation of the kinase is mediated by the ferredoxin–thioredoxin system and that a disulfide bond in the kinase rather than in the substrate may be the target site of thioredoxin [37,38]. In this respect, the N-terminal region of the kinase contains indeed two Cys residues, which are conserved in all species examined [23,24]. Both of these Cys are essential for the kinase activity because changes of either Cys through site-directed mutagenesis abolish the kinase activity . It is noticeable that these Cys are located on the lumen side of the thylakoid membrane whereas the kinase catalytic domain is on the stromal side where the substrate sites of the LHCII proteins are located [23,25] (Figure 2). Although the conserved Cys residues in the lumen are on the opposite side of the stromal thioredoxin according to this model, one possibility is that thiol-reducing equivalents are transferred across the thylakoid membrane through the CcdA and Hcf164 proteins, which operate in this way during heme and Cyt
The Stt7/STN7 kinase is associated with the Cyt
It is known that the activation of the kinase is intimately connected to the docking of plastoquinone to the Qo site of the Cyt
Another proposal for the mechanism of activation of the Stt7/STN7 kinase is that hydrogen peroxide may be involved by oxidizing the luminal C1 and C2 to form intra- and/or intermolecular disulfide bridges. It is based on the observation that singlet oxygen generated by PSII can oxidize plastoquinol with concomitant production of hydrogen peroxide in the thylakoid membranes . However, this proposal is difficult to reconcile with the observation that these Cys exist mostly in the oxidized form and the conversion from intra- to intermolecular disulfide bridges appears to be only transient .
State transitions involve remodeling of the antenna system of PSII within the thylakoid membranes. This poses a challenging problem especially considering the fact that among biological membranes, the thylakoid membrane is very crowded with 70% of the surface area of grana membranes occupied by proteins and 30% by lipids . Light-induced architectural changes in the folding of the thylakoid membrane are induced at least partly by changes in phosphorylation of thylakoid proteins catalyzed by the protein kinases Stt7/STN7 and Stl1/STN8, which most likely facilitate mobility of proteins in these membranes [52,53]. These two kinases appear to play an important role in chloroplast signaling in response to changing environmental conditions (Figure 3). Light irradiance, ambient CO2 level and the cellular ATP/ADP ratio modulate the redox state of the plastoquinone pool of the electron transport chain which is sensed by the Stt7/STN7 kinase. Together with the Stl1/STN8 kinase and the two corresponding protein phosphatases PPH1/TAP38 and PBCP, Stt7/STN7 forms a central quartet which orchestrates the phosphorylation of the LHCII and the PSII core proteins (Figure 3). PTK is another chloroplast Ser/Thr kinase of the casein kinase II family which is associated with the plastid RNA polymerase and acts as a global regulator of chloroplast transcription [54,55]. The CSK kinase shares structural features with cyanobacterial sensor histidine kinases and is conserved in all major plant and algal lineages except
The redox state of the PQ pool is modulated by the light irradiance, ATP/ADP ratio and ambient CO2 level. The protein kinases Stl1/STN8, Stt7/STN7, CSK, PTK and TAK1  are shown with their targets indicated by arrows.
2.2. Non photochemical quenching
While state transitions are mainly involved in low light responses through an extensive reorganization of the antenna systems, other mechanisms for the regulation of light-harvesting operate when oxygenic photosynthetic organisms are suddenly exposed to large and sudden changes in light intensity in their natural habitat. In the case of aquatic algae, even moderate water mixing can bring algae from full darkness to high light within minutes [59,60]. Under these conditions, increased electron flow along the electron transport chain generates a large proton gradient. The resulting acidification of the thylakoid lumen leads to the de-excitation of singlet excited light-harvesting pigments and is measured as non-photochemical quenching (NPQ of chlorophyll fluorescence). NPQ comprises several components; the major one is the high energy state quenching qE, which leads to the harmless heat dissipation of the absorbed excess light energy [20,61]. The other components which also contribute to fluorescence quenching are the photoinhibitory quenching qI and state transitions qT although qT is not associated with thermal dissipation of excitation energy. The qE mechanism occurs in all major algal taxa and land plants. However, the underlying molecular mechanisms of heat dissipation of excess excitation energy differ. The qE process involves both the xanthophyll cycle and the PsbS protein in plants. Another protein, LhcsR, has been shown to mediate qE in algae [19,62].
The proton gradient acts as a sensor of the state of the photosynthetic electron transport chain. The magnitude of this gradient is low under low light illumination and high under illumination with high light especially when it exceeds the capacity of the photosynthetic apparatus. The resulting acidification of the thylakoid lumen activates the xanthophyll cycle in which violaxanthin is de-epoxidized to zeaxanthin, a reaction catalyzed by violaxanthin de-epoxidase (VDE) which has an acidic pH optimum . The reverse reaction is catalyzed by zeaxanthin epoxidase with a broad pH optimum and which in contrast to VDE is active both in the dark and in the light. Because the turnover of this enzyme is considerably lower than that of VDE, zeaxanthin accumulates rapidly during high light illumination. The zeaxanthin-dependent NPQ depends greatly on the grana structure as unstacking of the membranes abolishes qE. It was proposed that the organization of LHCII in an aggregated state within the stacked grana region is essential for efficient qE . Both high proton concentration in the lumen and accumulation of zeaxanthin promote not only aggregation of LHCII but also that of the minor PSII antenna proteins CP29, CP26 and CP24 [65,66]. In plants, qE occurs in the LHC proteins at multiple sites of the antenna system . These proteins have the ability to switch from an efficient light-harvesting mode to a light energy dissipating state . Several mechanisms have been proposed including excitonic coupling, charge transfer and energy transfer between carotenoids and chlorophylls as well as chlorophyll–chlorophyll charge transfer states (for review see Ref. 20).
Another important player involved in NPQ is PsbS, a four-helix member of the LHC protein family . However, this protein does not appear to bind pigments although a chlorophyll molecule was detected at the dimer interface in the PsbS crystals . This protein appears to act as a sensor of the lumen pH most likely through protonation of its acidic lumen residues which in turn induces a rearrangement of the light-harvesting system required for induction of NPQ [71–73]. In this sense, PsbS would act as an antenna organizer, a view which is further supported by the fact that it is mobile in the thylakoid membrane , and it is able to associate with both the PSII core complex and LHCII . Moreover, qE can be switched on without the PsbS protein if the lumen pH is very low . It thus appears that protonated PsbS allows for a fast and efficient rearrangement of the PSII antenna which is still possible in its absence but requires a longer time.
NPQ has also been investigated in diatoms, a ubiquitous group of unicellular marine algae which make an important contribution to the global carbon assimilation . Diatoms acquired their chloroplast through secondary endosymbiosis from a red algal ancestor . In these organisms, similar to plants and green algae, qE relies on three interacting components, the light-induced proton gradient across the thylakoid membrane, the conversion of the xanthophyll diadinoxanthin (Dd) to diatoxanthin (Dt) catalyzed by the enzyme Dd-de-epoxidase which depends on a transthylakoid proton gradient and the Lhcx antenna proteins (for review see Ref. 87). Among these, Lhcx1 appears to play a major role in qE as changes in its level are directly related to the quenching of light energy . Lhcx1 also plays an important general role in light responses in diatoms as it accumulates in different amounts in ecotypes originating from different latitudes. In contrast to land plants, the proton gradient is unable to induce NPQ on its own in diatoms. It is only required to activate the de-epoxidation of Dd. The qE process represents an important photoprotective mechanism and involves a reorganization of the antenna complexes of diatoms . However, the quenching sites within the antenna systems of these organisms have not yet been precisely determined.
Another original feature of diatoms is the way they adjust the ATP/NADPH ratio which is important for proper carbon assimilation by the CBC and for optimal growth. In plants and green algae, this ratio is mainly set by the relative contributions of LEF and CEF and by the water-to-water cycles , whereas in diatoms this ratio relies principally on energetic exchanges between plastids and mitochondria . These bidirectional organellar interactions involve the rerouting of reducing power generated by photosynthesis in the plastids to mitochondria and the import of ATP produced in the mitochondria to the plastids.
2.3. PSII repair cycle
Water splitting by PSII is one of the strongest oxidizing reactions which occurs in living organisms. As a result, photodamage to PSII is unavoidable. A remarkable feature of this system is that it is efficiently repaired . PSII exists as a dimer in which each monomer consists of 28 subunits generally associated with two LHCII trimers in a supercomplex . The PSII core consists of the two reaction center polypeptides D1 and D2 which form a central heterodimer which acts as ligand for the chlorophyll dimer P680 and the other redox components including the quinones QA and QB, the primary and secondary electron acceptors. Among all PSII subunits, D1 is the major target of photodamage and needs to be specifically replaced. This process, called PSII repair cycle, involves the partial disassembly of the PSII supercomplex, the removal and degradation of the damaged D1 protein, its replacement by a newly synthesized copy and the reassembly of the PSII complex (Figure 4) . An important feature of this repair cycle is that it is compartmentalized within the crowded thylakoid membrane . Whereas damage of D1 occurs in the stacked grana region where most of PSII is located, the replacement of this protein takes place in the stroma lamellae. Although the exact role of phosphorylation is not fully understood, the current view is that the PSII repair cycle starts with phosphorylation of the PSII core subunits D1, D2, CP43 and PsbH mediated by the STN8 kinase [94,95] which leads to the disassembly of the PSII-LHCII supercomplex thereby allowing PSII to move to the grana margins and stroma lamellae [96,97]. Dephosphorylation by the PSII core phosphatase Pbcp  and by other unknown phosphatases is followed by the degradation of D1 by the FtsH and Deg proteases and a newly synthesized D1 is cotranslationally inserted into the PSII complex . Finally, the reassembled PSII complex moves back to the grana and reforms a supercomplex with LHCII. To make this cycle efficient, it is essential that the enzymes involved are confined to distinct thylakoid membrane subcompartments. Thus, protein degradation occurs on the grana margins and protein synthesis on the stroma lamellae. Additionally, partial conversion of grana stacks to grana margins allows the proteases to access PSII .
High light illumination leads to photooxidative damage of the PSII reaction center, especially the D1 protein. The PSII core proteins are phosphorylated and the damaged complex migrates from the grana (G) to the stromal lamellae (SL). The D1 protein is degraded by the FtsH and Deg proteases and upon its removal from the PSII reaction center a newly synthesized D1 protein is inserted cotranslationally into the complex which moves back to the grana and thereby completes the repair cycle. Reproduced from Ref. 5 with permission.
D1 degradation is significantly retarded in the
3. Response of the photosynthetic apparatus to micronutrient depletion
The photosynthetic machinery comprises several protein–pigment complexes with specific cofactors including iron, copper, manganese and iron–sulfur centers. Under conditions of limitation of one of these micronutrients, the photosynthetic machinery displays a remarkable plasticity and ability to adapt to its new environment.
3.1. Copper deficiency
3.2. Iron deficiency
Iron deficiency occurs often in nature and poses a challenge for photosynthetic organisms because of the abundance and importance of iron in the primary photosynthetic reactions. With its three 4Fe-4S centers, PSI is a prime target under these conditions. Under conditions of iron limitation, the level of PSI decreases when
Marine organisms can face iron limitation in the oceans. A deep-sea/ low light strain of the marine green alga
Micronutrient limitation can also act at the level of the biosynthesis of the photosynthetic apparatus which is mediated by the concerted action of the nuclear and chloroplast genetic systems. It is well established that subunits of the photosynthetic complexes originate from these two systems. In addition, a large number of nucleus-encoded factors are required for chloroplast gene expression that act at various plastid posttranscriptional steps comprising RNA processing and stability, translation and assembly of the photosynthetic complexes. Many of these factors have unique gene targets in the plastid and often interact directly or indirectly with specific 5′-untranslated RNA sequences . One of these factors, Taa1 is specifically required for the translation of the PsaA PSI reaction center subunit in
Similar findings have been reported for Mca1 and Tca1, two nucleus-encoded proteins that are required for the stability and translation of the
3.3. Sulfur deprivation and hydrogen production
Many soil-dwelling algae like
4. Long-term response: changes in nuclear and chloroplast gene
While short-term responses of the photosynthetic apparatus involve mostly posttranslational mechanisms such as phosphorylation or changes in pH and ion levels, long-term responses are mediated through changes in the expression of specific chloroplast and nuclear genes and their products. Environmental changes such as changes in light quantity and quality lead to changes in the state of the chloroplast which are perceived by the nucleus through a signaling chain referred to as retrograde signaling. The components of this signaling chain are still largely unknown although a few potential retrograde signals have been identified . Among these, tetrapyrroles appear to play a significant role. These compounds are involved in the chlorophyll biosynthetic pathway which needs to be tightly regulated to avoid photooxidative damage. Mg-protoporphyrin IX (Mg-Proto) was first shown to be involved in the repression of the LHCII genes in retrograde signaling in
The synthesis of tetrapyrroles needs to be tightly controlled because some of these chlorophyll or heme precursors are very photodynamic and can cause serious photooxidative damage. In land plants, the conversion of protochlorophyllide (PChlide) to chlorophyllide (Chlide) is light dependent. In the dark, overaccumulation of PChlide is prevented through a negative feedback mediated by the Flu protein which inhibits glutamyl-tRNA reductase at an early step of the tetrapyrrole pathway (Figure 5) . Although
The heme and chlorophyll biosynthetic pathways branch at protoporphyrin IX (Prot IX). GTR, glutamine tRNA reductase, is subjected to feedback inhibition by heme and FLU. In most land plants, conversion of PChlide (protochlorophyllide) to Chlide is light-dependent (L, in
Additional evidence for the involvement of tetrapyrroles in retrograde signaling comes from the identification of a functional bilin biosynthesis pathway in
A further striking example of the action of tetrapyrroles as mediators for plastid-to-nucleus-communication is the identification of a tetrapyrrole-regulated ubiquitin ligase for cell cycle coordination from organelle to nuclear DNA replication in the red alga
Redox changes within the photosynthetic electron transport chain occur upon changes in light quality and quantity, CO2 levels, nutrient availability and elevated temperature. As a result of unequal excitation of PSI and PSII or of insufficient electron acceptor capacity on the PSI acceptor side, the redox state of the plastoquinone pool is altered. In this case, chloroplast gene expression is affected in land plants  although the evidence is less convincing in algae. However, in these organisms, there is unambiguous evidence that nuclear gene expression is affected . A possible candidate for sensing the redox state of the plastoquinone pool is the chloroplast protein kinase Stt7/STN7 which is known to be activated when plastoquinol occupies the Qo site of the Cyt
In all situations in which the redox poise of the plastoquinone pool is affected, the relative sizes of the PSII and PSI antenna sizes play an important role. Several factors involved in antenna size were identified through a genetic screen in
Another protein regulating antenna size in
5. Conclusions and perspectives
The photosynthetic apparatus is a complex machinery consisting of several large protein–pigment complexes whose components are encoded by both nuclear and chloroplast genes. Thus, the biosynthesis of this system involves two distinct genetic systems which act in a coordinate manner. In nature, photosynthetic organisms are subjected to continuous environmental changes and need to adapt so as to maintain optimal photosynthetic activity and to protect themselves from photooxidative damage. These processes can be grouped in short-term and long-term responses. The first occurs in the second-to-minute range and involves light-induced protein conformational changes, posttranslational protein modifications, cell compartment–specific pH changes and ion fluxes across the chloroplast and thylakoid membranes. The second occurs in the minute-to-hour range and involves changes in gene expression and protein accumulation, which depend on an intricate bilateral communication system between chloroplasts and nucleus. Many nuclear genes encoding chloroplast proteins have been identified which are required for chloroplast gene expression and act mainly at posttranscriptional steps. Some of these factors appear to act constitutively while others assume a regulatory role because they have short half-lives and their level varies greatly upon changes in environmental cues including light, temperature and nutrient availability. However, the molecular mechanisms underlying the intercompartmental communication between chloroplast, mitochondria and nucleus are still largely unknown although several retrograde signals have been identified. They involve specific compounds such as tetrapyrroles and isoprenoids as well as plastid protein synthesis, the redox state of the photosynthetic electron transport chain and ROS generated under specific stress conditions. Moreover, a complex signaling network is operating within chloroplasts comprising several protein kinases and phosphatases, ion channels, and specific metabolites which act as signals and for the communication between chloroplast and nucleus. However, the signaling chains connecting these different components are still largely unknown and their identification remains an important challenge for future research.
The flexibility of the thylakoid membrane is truly remarkable. Although it is crowded with proteins, it still allows for efficient remodeling of the photosynthetic complexes within the thylakoid membrane especially in response to changes in the quality and quantity of light. Among these responses, state transitions and NPQ have been studied extensively and some of the underlying molecular mechanisms have been elucidated. However, many questions remain open. We still do not fully understand how the Stt7/STN7 kinase that plays a central role in state transitions and chloroplast signaling is activated and inactivated as a result of perturbations of the chloroplast redox poise. From an evolutionary point of view, it is particularly interesting to compare these adaptive responses in different photosynthetic organisms such as plants, fresh water and marine algae and cyanobacteria. In this respect, NPQ, the dissipation of excess excitation energy as heat in the light-harvesting systems of the photosystems, is of great importance and it is widely used in the plant kingdom. Recent studies on NPQ in different photosynthetic organisms raise several questions regarding the evolution of this essential photoprotective mechanism. For example, it is not clear why the Lhcsr proteins were lost during the transition from aquatic to land plants. Moreover, the qE process in most algae derived by secondary endosymbiosis from a red algal ancestor differs from that in extant red algae. All of these derived algae possess a xanthophyll cycle and Lhcsr-related proteins which are apparently absent in red algae  and which have been suggested to be derived from green algae [143,144]. It will clearly be important and challenging to elucidate these evolutionary puzzles.
I thank Nicolas Roggli for preparing the figures and Michel Goldschmidt-Clermont for critical reading of the manuscript. Work in the author’s laboratory was supported by grants from the Swiss National Science Foundation.