Cooperative D1 degradation in the photosystem II repair mediated by chloroplastic proteases in Arabidopsis

The mechanisms of photoinhibition and repair in plants under high light conditions and interplay with abiotic stressors

This review comprehensively examines the phenomenon of photoinhibition in plants, focusing mainly on the intricate relationship between photodamage and photosystem II (PSII) repair and the role of PSII extrinsic proteins and protein phosphorylation in these processes. In natural environments, photoinhibition occurs together with a suite of concurrent stress factors, including extreme temperatures, drought and salinization. Photoinhibition, primarily caused by high irradiance, results in a critical imbalance between the rate of PSII photodamage and its repair. Central to this process is the generation of reactive oxygen species (ROS), which not only impair the photosynthetic apparatus first PSII but also play a signalling role in chloroplasts and other cellulular structures. ROS generated under stress conditions inhibit the repair of photodamaged PSII by suppressing D1 protein synthesis and affecting PSII protein phosphorylation. Furthermore, this review considers how environmental stressors exacerbate PSII damage by interfering with PSII repair primarily by reducing de novo protein synthesis. In addition to causing direct damage, these stressors also contribute to ROS production by restricting CO2 fixation, which also reduces the intensity of protein synthesis. This knowledge has significant implications for agricultural practices and crop improvement under stressful conditions.

Characterization of tryptophan oxidation affecting D1 degradation by FtsH in the photosystem II quality control of chloroplasts

Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH.

Environmental gradients reveal stress hubs pre-dating plant terrestrialization

Plant terrestrialization brought forth the land plants (embryophytes). Embryophytes account for most of the biomass on land and evolved from streptophyte algae in a singular event. Recent advances have unravelled the first full genomes of the closest algal relatives of land plants; among the first such species was Mesotaenium endlicherianum. Here we used fine-combed RNA sequencing in tandem with a photophysiological assessment on Mesotaenium exposed to a continuous range of temperature and light cues. Our data establish a grid of 42 different conditions, resulting in 128 transcriptomes and ~1.5 Tbp (~9.9 billion reads) of data to study the combinatory effects of stress response using clustering along gradients. Mesotaenium shares with land plants major hubs in genetic networks underpinning stress response and acclimation. Our data suggest that lipid droplet formation and plastid and cell wall-derived signals have denominated molecular programmes since more than 600 million years of streptophyte evolution-before plants made their first steps on land.

Chloroplast SRP54 and FtsH protease coordinate thylakoid membrane-associated proteostasis in Arabidopsis

Thylakoid membrane protein quality control (PQC), which requires the coordination of membrane protein translocation and degradation of unassembled proteins, determines chloroplast development during de-etiolation. Despite numerous efforts, the regulation of this process in land plants is largely unknown. Here, we report the isolation and characterization of pale green Arabidopsis4 (pga4) mutants in Arabidopsis (Arabidopsis thaliana) with defects in chloroplast development during de-etiolation. Map-based cloning and complementation assays confirmed that PGA4 encodes the chloroplast Signal Recognition Particle 54 kDa (cpSRP54) protein. A heterogeneous Light-Harvesting Chlorophyll a/b Binding-Green Fluorescent Protein (LhcB2-GFP) fusion protein was generated as an indicative reporter for cpSRP54-mediated thylakoid translocation. LhcB2-GFP was dysfunctional and degraded to a short-form dLhcB2-GFP during de-etiolation through an N-terminal degradation initiated on thylakoid membranes. Further biochemical and genetic evidence demonstrated that the degradation of LhcB2-GFP to dLhcB2-GFP was disrupted in pga4 and yellow variegated2 (var2) mutants caused by mutations in the Filamentous Temperature-Sensitive H2 (VAR2/AtFtsH2) subunit of thylakoid FtsH. The yeast two-hybrid assay showed that the N-terminus of LhcB2-GFP interacts with the protease domain of VAR2/AtFtsH2. Moreover, the over-accumulated LhcB2-GFP in pga4 and var2 formed protein aggregates, which were insoluble in mild nonionic detergents. Genetically, cpSRP54 is a suppressor locus for the leaf variegation phenotype of var2. Together, these results demonstrate the coordination of cpSRP54 and thylakoid FtsH in maintaining thylakoid membrane PQC during the assembly of photosynthetic complexes and provide a trackable substrate and product for monitoring cpSRP54-dependent protein translocation and FtsH-dependent protein degradation.

Silencing of Pepper CaFtsH1 or CaFtsH8 Genes Alters Normal Leaf Development

Filamentation temperature-sensitive H (FtsH) is a proteolytic enzyme that plays an important role in plant photomorphogenesis and stress resistance. However, information regarding the FtsH family genes in pepper is limited. In our research, through genome-wide identification, 18 members of the pepper FtsH family (including five FtsHi members) were identified and renamed based on phylogenetic analysis. CaFtsH1 and CaFtsH8 were found to be essential for pepper chloroplast development and photosynthesis because FtsH5 and FtsH2 were lost in Solanaceae diploids. We found that the CaFtsH1 and CaFtsH8 proteins were located in the chloroplasts and specifically expressed in pepper green tissues. Meanwhile, CaFtsH1 and CaFtsH8-silenced plants created by virus-induced gene silencing exhibited albino leaf phenotypes. In addition, CaFtsH1-silenced plants were observed to contain very few dysplastic chloroplasts and lost the capacity for photoautotrophic growth. Transcriptome analysis revealed that the expression of chloroplast-related genes such as those coding the photosynthesis-antenna protein and structural proteins was downregulated in CaFtsH1-silenced plants, resulting in the inability to form normal chloroplasts. This study improves our understanding of pepper chloroplast formation and photosynthesis through the identification and functional study of CaFtsH genes.

Immunophilin CYN28 is required for accumulation of photosystem II and thylakoid FtsH protease in Chlamydomonas

Excess light causes severe photodamage to photosystem II (PSII) where the primary charge separation for electron transfer takes place. Dissection of mechanisms underlying the PSII maintenance and repair cycle in green algae promotes the usage of genetic engineering and synthetic biology to improve photosynthesis and biomass production. In this study, we systematically analyzed the high light (HL) responsive immunophilin genes in Chlamydomonas (Chlamydomonas reinhardtii) and identified one chloroplast lumen-localized immunophilin, CYN28, as an essential player in HL tolerance. Lack of CYN28 caused HL hypersensitivity, severely reduced accumulation of PSII supercomplexes and compromised PSII repair in cyn28. The thylakoid FtsH (filamentation temperature-sensitive H) is an essential AAA family metalloprotease involved in the degradation of photodamaged D1 during the PSII repair cycle and was identified as one potential target of CYN28. In the cyn28 mutant, the thylakoid FtsH undergoes inefficient turnover under HL conditions. The CYN28-FtsH1/2 interaction relies on the FtsH N-terminal proline residues and is strengthened particularly under HL. Further analyses demonstrated CYN28 displays peptidyl-prolyl isomerase (PPIase) activity, which is necessary for its physiological function. Taken together, we propose that immunophilin CYN28 participates in PSII maintenance and regulates the homeostasis of FtsH under HL stress via its PPIase activity.

Rubredoxin 1 promotes the proper folding of D1 and is not required for heme b559 assembly in Chlamydomonas photosystem II

Photosystem II (PSII), the water:plastoquinone oxidoreductase of oxygenic photosynthesis, contains a heme b₅₅₉ iron whose axial ligands are provided by histidine residues from the α (PsbE) and β (PsbF) subunits. PSII assembly depends on accessory proteins that facilitate the step-wise association of its protein and pigment components into a functional complex, a process that is challenging to study due to the low accumulation of assembly intermediates. Here, we examined the putative role of the iron[1Fe-0S]-containing protein rubredoxin 1 (RBD1) as an assembly factor for cytochrome b₅₅₉, using the RBD1-lacking 2pac mutant from Chlamydomonas reinhardtii, in which the accumulation of PSII was rescued by the inactivation of the thylakoid membrane FtsH protease. To this end, we constructed the double mutant 2pac ftsh1-1, which harbored PSII dimers that sustained its photoautotrophic growth. We purified PSII from the 2pac ftsh1-1 background and found that α and β cytochrome b₅₅₉ subunits are still present and coordinate heme b₅₅₉ as in the WT. Interestingly, immunoblot analysis of dark- and low light-grown 2pac ftsh1-1 showed the accumulation of a 23-kDa fragment of the D1 protein, a marker typically associated with structural changes resulting from photodamage of PSII. Its cleavage occurs in the vicinity of a nonheme iron which binds to PSII on its electron acceptor side. Altogether, our findings demonstrate that RBD1 is not required for heme b₅₅₉ assembly and point to a role for RBD1 in promoting the proper folding of D1, possibly via delivery or reduction of the nonheme iron during PSII assembly.

Chloroplast proteostasis: A story of birth, life, and death

Protein homeostasis (proteostasis) is a dynamic balance of protein synthesis and degradation. Because of the endosymbiotic origin of chloroplasts and the massive transfer of their genetic information to the nucleus of the host cell, many protein complexes in the chloroplasts are constituted from subunits encoded by both genomes. Hence, the proper function of chloroplasts relies on the coordinated expression of chloroplast- and nucleus-encoded genes. The biogenesis and maintenance of chloroplast proteostasis are dependent on synthesis of chloroplast-encoded proteins, import of nucleus-encoded chloroplast proteins from the cytosol, and clearance of damaged or otherwise undesired "old" proteins. This review focuses on the regulation of chloroplast proteostasis, its interaction with proteostasis of the cytosol, and its retrograde control over nuclear gene expression. We also discuss significant issues and perspectives for future studies and potential applications for improving the photosynthetic performance and stress tolerance of crops.

Effects of High Irradiance and Low Water Temperature on Photoinhibition and Repair of Photosystems in Marimo (Aegagropila linnaei) in Lake Akan, Japan

The green alga Aegagropila linnaei often forms spherical aggregates called "marimo" in Lake Akan in Japan. In winter, marimo are exposed to low water temperatures at 1-4 °C but protected from strong sunlight by ice coverage, which may disappear due to global warming. In this study, photoinhibition in marimo was examined at 2 °C using chlorophyll fluorescence and 830 nm absorption. Filamentous cells of A. linnaei dissected from marimo were exposed to strong light at 2 °C. Photosystem II (PSII) was markedly photoinhibited, while photosystem I was unaffected. When the cells with PSII damaged by the 4 h treatment were subsequently illuminated with moderate repair light at 2 °C, the maximal efficiency of PSII was recovered to the level before photoinhibition. However, after the longer photoinhibitory treatments, PSII efficiency did not recover by the repair light. When the cells were exposed to simulated diurnal light for 12 h per day, which was more ecological, the cells died within a few days. Our results showed new findings of the PSII repair at 2 °C and serious damage at the cellular level from prolonged high-light treatments. Further, we provided a clue to what may happen to marimo in Lake Akan in the near future.

The Arabidopsis NLP7-HB52/54-VAR2 pathway modulates energy utilization in diverse light and nitrogen conditions

In plants, nitrate is the dominant nitrogen (N) source and a critical nutrient signal regulating various physiological and developmental processes.^1,2,3,4 Nitrate-responsive gene regulatory networks are widely believed to control growth, development, and life cycle in addition to N acquisition and utilization,^1,2,3,4 and NIN-LIKE PROTEIN (NLP) transcriptional activators have been identified as the master regulators governing the networks.^5,6,7 However, it remains to be elucidated how nitrate signaling regulates respective physiological and developmental processes. Here, we have identified a new nitrate-activated transcriptional cascade involved in chloroplast development and the maintenance of chloroplast function in Arabidopsis. This cascade consisting of NLP7 and two homeodomain-leucine zipper (HD-Zip) class I transcription factors, HOMEOBOX PROTEIN52 (HB52) and HB54,^8,9 was responsible for nitrate- and light-dependent expression of VAR2 encoding the FtsH2 subunit of the chloroplast FtsH protease involved in the quality control of photodamaged thylakoid membrane proteins.^10,11 Consistently, the nitrate-activated NLP7-HB52/54-VAR2 pathway underpinned photosynthetic light energy utilization, especially in high light environments. Furthermore, genetically enhancing the NLP7-HB52/54-VAR2 pathway resulted in improved light energy utilization under high light and low N conditions, a superior agronomic trait. These findings shed light on a new role of nitrate signaling and a novel mechanism for integrating information on N nutrient and light environments, providing a hint for enhancing the light energy utilization of plants in low N environments.

Melatonin as a regulator of plant ionic homeostasis: implications for abiotic stress tolerance

Melatonin is a highly conserved and ubiquitous molecule that operates upstream of a broad array of receptors in animal systems. Since melatonin was discovered in plants in 1995, hundreds of papers have been published revealing its role in plant growth, development, and adaptive responses to the environment. This paper summarizes the current state of knowledge of melatonin's involvement in regulating plant ion homeostasis and abiotic stress tolerance. The major topics covered here are: (i) melatonin's control of H+-ATPase activity and its implication for plant adaptive responses to various abiotic stresses; (ii) regulation of the reactive oxygen species (ROS)-Ca2+ hub by melatonin and its role in stress signaling; and (iii) melatonin's regulation of ionic homeostasis via hormonal cross-talk. We also show that the properties of the melatonin molecule allow its direct scavenging of ROS, thus preventing negative effects of ROS-induced activation of ion channels. The above 'desensitization' may play a critical role in preventing stress-induced K+ loss from the cytosol as well as maintaining basic levels of cytosolic Ca2+ required for optimal cell operation. Future studies should focus on revealing the molecular identity of transporters that could be directly regulated by melatonin and providing a bioinformatic analysis of evolutionary aspects of melatonin sensing and signaling.

Mixed population hypothesis of the active and inactive PSII complexes opens a new door for photoinhibition and fluorescence studies: an ecophysiological perspective

The current hypotheses for the mechanisms of photosystem II (PSII) photodamage in vivo remain split on the primary damage site. However, most researchers have considered that PSII is inhibited by a sole mechanism and that the photoinhibited PSII consists of one population. In this perspective, we propose 'the mixed population hypothesis', in which there are four PSII populations: PSII with active/inactive Mn4 CaO5 oxygen-evolving complex respectively with functional/damaged primary quinone (QA ) reduction activity. This hypothesis provides a new insight into not only the PSII photoinhibition/photoprotection studies but also the repair process. We discuss our new data implying that the repair rate differs in the respective PSII populations.

Chloroplasts Protein Quality Control and Turnover: A Multitude of Mechanisms

As the organelle of photosynthesis and other important metabolic pathways, chloroplasts contain up to 70% of leaf proteins with uniquely complex processes in synthesis, import, assembly, and turnover. Maintaining functional protein homeostasis in chloroplasts is vitally important for the fitness and survival of plants. Research over the past several decades has revealed a multitude of mechanisms that play important roles in chloroplast protein quality control and turnover under normal and stress conditions. These mechanisms include: (i) endosymbiotically-derived proteases and associated proteins that play a vital role in maintaining protein homeostasis inside the chloroplasts, (ii) the ubiquitin-dependent turnover of unimported chloroplast precursor proteins to prevent their accumulation in the cytosol, (iii) chloroplast-associated degradation of the chloroplast outer-membrane translocon proteins for the regulation of chloroplast protein import, (iv) chloroplast unfolded protein response triggered by accumulated unfolded and misfolded proteins inside the chloroplasts, and (v) vesicle-mediated degradation of chloroplast components in the vacuole. Here, we provide a comprehensive review of these diverse mechanisms of chloroplast protein quality control and turnover and discuss important questions that remain to be addressed in order to better understand and improve important chloroplast functions.

Genetic analysis of chlorophyll synthesis and degradation regulated by BALANCE of CHLOROPHYLL METABOLISM

Chlorophyll (Chl) serves a number of essential functions, capturing and converting light energy as a component of photosystem supercomplexes. Chl degradation during leaf senescence is also required for adequate degeneration of chloroplasts and salvaging of nutrients from senescent leaves. In this study, we performed genetic analysis to determine the functions of BALANCE of CHLOROPHYLL METABOLISM1 (BCM1) and BCM2, which control Chl levels by regulating synthesis and degradation, and STAY-GREEN (SGR)1 (also known as NON-YELLOWING1 [NYE1]) and SGR2, which encode Mg-dechelatase and catalyze Chl a degradation in Arabidopsis (Arabidopsis thaliana). Analysis of bcm1 bcm2 revealed that both BCM1 and BCM2 are involved in the regulation of Chl levels in presenescent leaves and Chl degradation in senescing leaves. Analysis of bcm1 bcm2 nye1 nye2 suggested that BCMs repress Chl-degrading activity in both presenescent and senescing leaves by regulating SGR activity. Furthermore, transactivation analysis and chromatin immunoprecipitation (ChIP) assay revealed that GOLDEN2-LIKE1 (GLK1), a central transcription factor regulating the expression of genes encoding photosystem-related proteins, such as light-harvesting Chl a/b-binding proteins (LHCPs), directly regulates the transcription of BCM1. LHCPs are stabilized by Chl binding, suggesting that GLKs control the amount of LHCP through transcriptional and post-translational regulation via BCM-mediated Chl-level regulation. Meanwhile, we generated a mutant of the BCM ortholog in lettuce (Lactuca sativa) by genome editing and found that it showed an early yellowing phenotype, but only a slight reduction in Chl in presenescent leaves. Thus, this study revealed a conserved but slightly diversified regulation of Chl and LHCP levels via the GLK-BCM pathway in eudicots.

Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L

The availability and intensity of sunlight are among the major factors of growth, development and metabolism in plants. However, excessive illumination disrupts the electronic balance of photosystems and leads to the accumulation of reactive oxygen species in chloroplasts, further mediating several regulatory mechanisms at the subcellular, genetic, and molecular levels. We carried out a comprehensive bioinformatic analysis that aimed to identify genetic systems and candidate transcription factors involved in the response to high light stress in Arabidopsis thaliana L. using resources GEO NCBI, string-db, ShinyGO, STREME, and Tomtom, as well as programs metaRE, CisCross, and Cytoscape. Through the meta-analysis of five transcriptomic experiments, we selected a set of 1151 differentially expressed genes, including 453 genes that compose the gene network. Ten significantly enriched regulatory motifs for TFs families ZF-HD, HB, C2H2, NAC, BZR, and ARID were found in the promoter regions of differentially expressed genes. In addition, we predicted families of transcription factors associated with the duration of exposure (RAV, HSF), intensity of high light treatment (MYB, REM), and the direction of gene expression change (HSF, S1Fa-like). We predicted genetic components systems involved in a high light response and their expression changes, potential transcriptional regulators, and associated processes.

Brassica evolution of essential BnaFtsH1 genes involved in the PSII repair cycle and loss of FtsH5

The PSII repair cycle is an important part of photosynthesis and is essential for high photosynthetic efficiency. The study of essential genes in Brassica napus provides significant potential for the improvement of gene editing technology and molecular breeding design. Previously, we identified a B. napus lethal mutant (7-521Y), which was controlled by two recessive genes (cyd1 and cyd2). BnaC06.FtsH1 was identified as a CYD1 target gene through functional verification. In the present study, we employed fine-mapping, genetic complementation, and CRISPR/Cas9 experiments to identify BnaA07.FtsH1 as the target gene of CYD2, functioning similarly to BnaC06.FtsH1. By analyzing CRISPR/Cas9 T₁ generation plants of the Westar variety, we found that the copy number of FtsH1 was positively correlated with its biomass accumulation. Transcriptome analysis of cotyledons revealed differences in the expression of photosynthesis antenna and structural proteins between the mutant and complementary seedlings. Phylogenetic and chromosome linear analyses, based on 15 sequenced cruciferous species, revealed that Brassica alone had lost FtsH5 during evolution. This may be related to the fact that FtsH5 was located at the end of chromosome ABK8 in the ancestor species. Cloning and identification of BnaFtsH1s provide a deeper understanding of PSII repair cycle mechanisms and offer new insights for the improvement of photosynthetic efficiency and molecular breeding design in B. napus.

Recent Advances in Understanding the Structural and Functional Evolution of FtsH Proteases

The FtsH family of proteases are membrane-anchored, ATP-dependent, zinc metalloproteases. They are universally present in prokaryotes and the mitochondria and chloroplasts of eukaryotic cells. Most bacteria bear a single ftsH gene that produces hexameric homocomplexes with diverse house-keeping roles. However, in mitochondria, chloroplasts and cyanobacteria, multiple FtsH homologs form homo- and heterocomplexes with specialized functions in maintaining photosynthesis and respiration. The diversification of FtsH homologs combined with selective pairing of FtsH isomers is a versatile strategy to enable functional adaptation. In this article we summarize recent progress in understanding the evolution, structure and function of FtsH proteases with a focus on the role of FtsH in photosynthesis and respiration.

Photosystem II photoinhibition and photoprotection in a lycophyte, Selaginella martensii

The Lycophyte Selaginella martensii efficiently acclimates to diverse light environments, from deep shade to full sunlight. The plant does not modulate the abundance of the Light Harvesting Complex II, mostly found as a free trimer, and does not alter the maximum capacity of thermal dissipation (NPQ). Nevertheless, the photoprotection is expected to be modulatable upon long-term light acclimation to preserve the photosystems (PSII, PSI). The effects of long-term light acclimation on PSII photoprotection were investigated using the chlorophyll fluorometric method known as "photochemical quenching measured in the dark" (qP_d ). Singularly high-qP_d values at relatively low irradiance suggest a heterogeneous antenna system (PSII antenna uncoupling). The extent of antenna uncoupling largely depends on the light regime, reaching the highest value in sun-acclimated plants. In parallel, the photoprotective NPQ (pNPQ) increased from deep-shade to high-light grown plants. It is proposed that the differences in the long-term modulation in the photoprotective capacity are proportional to the amount of uncoupled LHCII. In deep-shade plants, the inconsistency between invariable maximum NPQ and lower pNPQ is attributed to the thermal dissipation occurring in the PSII core.

Molecular origins of induction and loss of photoinhibition-related energy dissipation qI

Photosynthesis fuels life on Earth using sunlight as energy source. However, light has a simultaneous detrimental effect on the enzyme triggering photosynthesis and producing oxygen, photosystem II (PSII). Photoinhibition, the light-dependent decrease of PSII activity, results in a major limitation to aquatic and land photosynthesis and occurs upon all environmental stress conditions. In this work, we investigated the molecular origins of photoinhibition focusing on the paradoxical energy dissipation process of unknown nature coinciding with PSII damage. Integrating spectroscopic, biochemical, and computational approaches, we demonstrate that the site of this quenching process is the PSII reaction center. We propose that the formation of quenching and the closure of PSII stem from the same event. We lastly reveal the heterogeneity of PSII upon photoinhibition using structure-function modeling of excitation energy transfer. This work unravels the functional details of the damage-induced energy dissipation at the heart of photosynthesis.

Chlamydomonas proteases: classification, phylogeny, and molecular mechanisms

Proteases can regulate myriad biochemical pathways by digesting or processing target proteins. While up to 3% of eukaryotic genes encode proteases, only a tiny fraction of proteases are mechanistically understood. Furthermore, most of the current knowledge about proteases is derived from studies of a few model organisms, including Arabidopsis thaliana in the case of plants. Proteases in other plant model systems are largely unexplored territory, limiting our mechanistic comprehension of post-translational regulation in plants and hampering integrated understanding of how proteolysis evolved. We argue that the unicellular green alga Chlamydomonas reinhardtii has a number of technical and biological advantages for systematic studies of proteases, including reduced complexity of many protease families and ease of cell phenotyping. With this end in view, we share a genome-wide inventory of proteolytic enzymes in Chlamydomonas, compare the protease degradomes of Chlamydomonas and Arabidopsis, and consider the phylogenetic relatedness of Chlamydomonas proteases to major taxonomic groups. Finally, we summarize the current knowledge of the biochemical regulation and physiological roles of proteases in this algal model. We anticipate that our survey will promote and streamline future research on Chlamydomonas proteases, generating new insights into proteolytic mechanisms and the evolution of digestive and limited proteolysis.

Photosystem I Inhibition, Protection and Signalling: Knowns and Unknowns

Photosynthesis is the process that harnesses, converts and stores light energy in the form of chemical energy in bonds of organic compounds. Oxygenic photosynthetic organisms (i.e., plants, algae and cyanobacteria) employ an efficient apparatus to split water and transport electrons to high-energy electron acceptors. The photosynthetic system must be finely balanced between energy harvesting and energy utilisation, in order to limit generation of dangerous compounds that can damage the integrity of cells. Insight into how the photosynthetic components are protected, regulated, damaged, and repaired during changing environmental conditions is crucial for improving photosynthetic efficiency in crop species. Photosystem I (PSI) is an integral component of the photosynthetic system located at the juncture between energy-harnessing and energy consumption through metabolism. Although the main site of photoinhibition is the photosystem II (PSII), PSI is also known to be inactivated by photosynthetic energy imbalance, with slower reactivation compared to PSII; however, several outstanding questions remain about the mechanisms of damage and repair, and about the impact of PSI photoinhibition on signalling and metabolism. In this review, we address the knowns and unknowns about PSI activity, inhibition, protection, and repair in plants. We also discuss the role of PSI in retrograde signalling pathways and highlight putative signals triggered by the functional status of the PSI pool.

Chloroplast dismantling in leaf senescence

In photosynthetic plant cells, chloroplasts act as factories of metabolic intermediates that support plant growth. Chloroplast performance is highly influenced by environmental cues. Thus, these organelles have the additional function of sensing ever changing environmental conditions, thereby playing a key role in harmonizing the growth and development of different organs and in plant acclimation to the environment. Moreover, chloroplasts constitute an excellent source of metabolic intermediates that are remobilized to sink tissues during senescence so that chloroplast dismantling is a tightly regulated process that plays a key role in plant development. Stressful environmental conditions enhance the generation of reactive oxygen species (ROS) by chloroplasts, which may lead to oxidative stress causing damage to the organelle. These environmental conditions trigger mechanisms that allow the rapid dismantling of damaged chloroplasts, which is crucial to avoid deleterious effects of toxic by-products of the degradative process. In this review, we discuss the effect of redox homeostasis and ROS generation in the process of chloroplast dismantling. Furthermore, we summarize the structural and biochemical events, both intra- and extraplastid, that characterize the process of chloroplast dismantling in senescence and in response to environmental stresses.

Characterization of the Free and Membrane-Associated Fractions of the Thylakoid Lumen Proteome in Arabidopsis thaliana

The thylakoid lumen houses proteins that are vital for photosynthetic electron transport, including water-splitting at photosystem (PS) II and shuttling of electrons from cytochrome b₆f to PSI. Other lumen proteins maintain photosynthetic activity through biogenesis and turnover of PSII complexes. Although all lumen proteins are soluble, these known details have highlighted interactions of some lumen proteins with thylakoid membranes or thylakoid-intrinsic proteins. Meanwhile, the functional details of most lumen proteins, as well as their distribution between the soluble and membrane-associated lumen fractions, remain unknown. The current study isolated the soluble free lumen (FL) and membrane-associated lumen (MAL) fractions from Arabidopsis thaliana, and used gel- and mass spectrometry-based proteomics methods to analyze the contents of each proteome. These results identified 60 lumenal proteins, and clearly distinguished the difference between the FL and MAL proteomes. The most abundant proteins in the FL fraction were involved in PSII assembly and repair, while the MAL proteome was enriched in proteins that support the oxygen-evolving complex (OEC). Novel proteins, including a new PsbP domain-containing isoform, as well as several novel post-translational modifications and N-termini, are reported, and bi-dimensional separation of the lumen proteome identified several protein oligomers in the thylakoid lumen.

Autophagy complements metalloprotease FtsH6 in degrading plastid heat shock protein HSP21 during heat stress recovery

Moderate and temporary heat stresses (HS) prime plants to tolerate, and survive, a subsequent severe HS. Such acquired thermotolerance can be maintained for several days under normal growth conditions, and create a HS memory. We recently demonstrated that plastid-localized small heat shock protein HSP21 is a key component of HS memory in Arabidopsis thaliana. A sustained high abundance of HSP21 during the HS recovery phase extends HS memory. The level of HSP21 is negatively controlled by plastid-localized metalloprotease FtsH6 during HS recovery. Here, we demonstrate that autophagy, a cellular recycling mechanism, exerts additional control over HSP21 degradation. Genetic and chemical disruption of both, metalloprotease activity and autophagy trigger superior HSP21 accumulation, thereby improving memory. Furthermore, we provide evidence that autophagy cargo receptor ATG8-INTERACTING PROTEIN1 (ATI1) is associated with HS memory. ATI1 bodies colocalize with both autophagosomes and HSP21, and their abundance and transport to the vacuole increase during HS recovery. Together, our results provide new insights into the control module for the regulation of HS memory, in which two distinct protein degradation pathways act in concert to degrade HSP21, thereby enabling cells to recover from the HS effect at the cost of reducing the HS memory.

H2O2 priming induces proteomic responses to defense against salt stress in maize

KEY MESSAGE

H₂O₂ priming reprograms essential proteins' expression to help plants survive, promoting responsive and unresponsive proteins adjustment to salt stress.

ABSTACRT

Priming is a powerful strategy to enhance abiotic stress tolerance in plants. Despite this, there is scarce information about the mechanisms induced by H₂O₂ priming for salt stress tolerance, particularly on proteome modulation. Improving maize cultivation in areas subjected to salinity is imperative for the local economy and food security. Thereby, this study aimed to investigate physiological changes linked with post-translational protein events induced by foliar H₂O₂ priming of Zea mays plants under salt stress. As expected, salt treatment promoted a considerable accumulation of Na⁺ ions, a 12-fold increase. It drastically affected growth parameters and relative water content, as well as promoted adverse alteration in the proteome profile, when compared to the absence of salt conditions. Conversely, H₂O₂ priming was beneficial via specific proteome reprogramming, which promoted better response to salinity by 16% reduction in Na⁺ content and shoots growth improvement, increasing 61% in dry mass. The identified proteins were associated with photosynthesis and redox homeostasis, critical metabolic pathways for helping plants survive in saline stress by the protection of chloroplasts organization and carbon fixation, as well as state redox. This research provides new proteomic data to improve understanding and forward identifying biotechnological strategies to promote salt stress tolerance.

Profiling thimet oligopeptidase-mediated proteolysis in Arabidopsis thaliana

Protein homeostasis (proteostasis) is crucial for proper cellular function, including the production of peptides with biological functions through controlled proteolysis. Proteostasis has roles in maintenance of cellular functions and plant interactions with the environment under physiological conditions. Plant stress continues to reduce agricultural yields causing substantial economic losses; thus, it is critical to understand how plants perceive stress signals to elicit responses for survival. As previously shown in Arabidopsis thaliana, thimet oligopeptidases (TOPs) TOP1 (also referred to as organellar oligopeptidase) and TOP2 (also referred to as cytosolic oligopeptidase) are essential components in plant response to pathogens, but further characterization of TOPs and their peptide substrates is required to understand their contributions to stress perception and defense signaling. Herein, label-free peptidomics via liquid chromatography-tandem mass spectrometry was used to differentially quantify 1111 peptides, originating from 369 proteins, between the Arabidopsis Col-0 wild type and top1top2 knock-out mutant. This revealed 350 peptides as significantly more abundant in the mutant, representing accumulation of these potential TOP substrates. Ten direct substrates were validated using in vitro enzyme assays with recombinant TOPs and synthetic candidate peptides. These TOP substrates are derived from proteins involved in photosynthesis, glycolysis, protein folding, biogenesis, and antioxidant defense, implicating TOP involvement in processes aside from defense signaling. Sequence motif analysis revealed TOP cleavage preference for non-polar residues in the positions surrounding the cleavage site. Identification of these substrates provides a framework for TOP signaling networks, through which the interplay between proteolytic pathways and defense signaling can be further characterized.

Deciphering the Proteotoxic Stress Responses Triggered by the Perturbed Thylakoid Proteostasis in Arabidopsis

Here, we explored heat dependent thylakoid FtsH protease substrates and investigated proteotoxicity induced by thermal damage and processive protease dysfunction on the thylakoid membrane. Through our thylakoid enriched proteome analysis and biochemical experiments, carbonylated stromal proteins were suggested as possible FtsH targets. Furthermore, we observed in the thylakoid fractions in the absence of FtsH stromal reactive oxygen species-detoxifying enzymes, as well as heat shock proteins and chaperones, which are known to be upregulated at the transcriptional level when this protease is absent, which is called the damaged protein response, resembling unfolded protein response in eukaryotic cells. Interestingly, the thylakoid-enriched high-density fractions included stromal translation factors and RNA-binding proteins, along with aminoacyl-tRNA synthetase, reminiscent of the formation of stress granules. Unexpectedly, extraplastid proteins such as mitochondrial chaperones, peroxidase, tricarboxylic acid cycle and respiratory chain enzymes, as well as cytosolic ribosomes, translation factors, heat shock proteins, antioxidants and metabolic enzymes, were also found deposited in the high-density fractions depending on the loss of thylakoid FtsH, with more prominent effects of thermal stress on the cytosolic proteins. This may reflect intracellular adaptation to the proteotoxic influences from the organelle.

Fine Mapping and Identification of BnaC06.FtsH1, a Lethal Gene That Regulates the PSII Repair Cycle in Brassica napus

Photosystem II (PSII) is an important component of the chloroplast. The PSII repair cycle is crucial for the relief of photoinhibition and may be advantageous when improving stress resistance and photosynthetic efficiency. Lethal genes are widely used in the efficiency detection and method improvement of gene editing. In the present study, we identified the naturally occurring lethal mutant 7-521Y with etiolated cotyledons in Brassica napus, controlled by double-recessive genes (named cyd1 and cyd2). By combining whole-genome resequencing and map-based cloning, CYD1 was fine-mapped to a 29 kb genomic region using 15,167 etiolated individuals. Through cosegregation analysis and functional verification of the transgene, BnaC06.FtsH1 was determined to be the target gene; it encodes an filamentation temperature sensitive protein H 1 (FtsH1) hydrolase that degrades damaged PSII D1 in Arabidopsis thaliana. The expression of BnaC06.FtsH1 was high in the cotyledons, leaves, and flowers of B. napus, and localized in the chloroplasts. In addition, the expression of EngA (upstream regulation gene of FtsH) increased and D1 decreased in 7-521Y. Double mutants of FtsH1 and FtsH5 were lethal in A. thaliana. Through phylogenetic analysis, the loss of FtsH5 was identified in Brassica, and the remaining FtsH1 was required for PSII repair cycle. CYD2 may be a homologous gene of FtsH1 on chromosome A07 of B. napus. Our study provides new insights into lethal mutants, the findings may help improve the efficiency of the PSII repair cycle and biomass accumulation in oilseed rape.

Expression of Flavodiiron Proteins Flv2-Flv4 in Chloroplasts of Arabidopsis and Tobacco Plants Provides Multiple Stress Tolerance

With the notable exception of angiosperms, all phototrophs contain different sets of flavodiiron proteins that help to relieve the excess of excitation energy on the photosynthetic electron transport chain during adverse environmental conditions, presumably by reducing oxygen directly to water. Among them, the Flv2-Flv4 dimer is only found in β-cyanobacteria and induced by high light, supporting a role in stress protection. The possibility of a similar protective function in plants was assayed by expressing Synechocystis Flv2-Flv4 in chloroplasts of tobacco and Arabidopsis. Flv-expressing plants exhibited increased tolerance toward high irradiation, salinity, oxidants, and drought. Stress tolerance was reflected by better growth, preservation of photosynthetic activity, and membrane integrity. Metabolic profiling under drought showed enhanced accumulation of soluble sugars and amino acids in transgenic Arabidopsis and a remarkable shift of sucrose into starch, in line with metabolic responses of drought-tolerant genotypes. Our results indicate that the Flv2-Flv4 complex retains its stress protection activities when expressed in chloroplasts of angiosperm species by acting as an additional electron sink. The flv2-flv4 genes constitute a novel biotechnological tool to generate plants with increased tolerance to agronomically relevant stress conditions that represent a significant productivity constraint.

Phos-tag-based approach to study protein phosphorylation in the thylakoid membrane

Protein phosphorylation is a fundamental post-translational modification in all organisms. In photoautotrophic organisms, protein phosphorylation is essential for the fine-tuning of photosynthesis. The reversible phosphorylation of the photosystem II (PSII) core and the light-harvesting complex of PSII (LHCII) contribute to the regulation of photosynthetic activities. Besides the phosphorylation of these major proteins, recent phosphoproteomic analyses have revealed that several proteins are phosphorylated in the thylakoid membrane. In this study, we utilized the Phos-tag technology for a comprehensive assessment of protein phosphorylation in the thylakoid membrane of Arabidopsis. Phos-tag SDS-PAGE enables the mobility shift of phosphorylated proteins compared with their non-phosphorylated isoform, thus differentiating phosphorylated proteins from their non-phosphorylated isoforms. We extrapolated this technique to two-dimensional (2D) SDS-PAGE for detecting protein phosphorylation in the thylakoid membrane. Thylakoid proteins were separated in the first dimension by conventional SDS-PAGE and in the second dimension by Phos-tag SDS-PAGE. In addition to the isolation of major phosphorylated photosynthesis-related proteins, 2D Phos-tag SDS-PAGE enabled the detection of several minor phosphorylated proteins in the thylakoid membrane. The analysis of the thylakoid kinase mutants demonstrated that light-dependent protein phosphorylation was mainly restricted to the phosphorylation of the PSII core and LHCII proteins. Furthermore, we assessed the phosphorylation states of the structural domains of the thylakoid membrane, grana core, grana margin, and stroma lamella. Overall, these results demonstrated that Phos-tag SDS-PAGE is a useful biochemical tool for studying in vivo protein phosphorylation in the thylakoid membrane protein.

Identification and Characterization of an Early Leaf Senescence Gene ELS1 in Soybean

Early leaf senescence phenotype in soybean could be helpful to shorten the maturation period and prevent green stem disorder. From a high-density mutation library, we identified two early leaf senescence soybean mutant lines, els1-1 (early leaf senescence 1) and els1-2. The chlorophyll contents of both els1-1 and els1-2 were low in pre-senescent leaves. They degraded rapidly in senescent leaves, revealing that ELS1 is involved in chlorophyll biosynthesis during leaf development and chlorophyll degradation during leaf senescence. The causal mutations in els1 were identified by next-generation sequencing-based bulked segregant analysis. ELS1 encodes the ortholog of the Arabidopsis CaaX-like protease BCM1, which is localized in chloroplasts. Soybean ELS1 was highly expressed in green tissue, especially in mature leaves. The accumulation of photosystem I core proteins and light-harvesting proteins in els1 was low even in pre-senescent leaves, and their degradation was accelerated during leaf senescence. These results suggest that soybean ELS1 is involved in both chlorophyll synthesis and degradation, consistent with the findings in Arabidopsis BCM1. The gene els1, characterized by early leaf senescence and subsequent early maturation, does not affect the flowering time. Hence, the early leaf senescence trait regulated by els1 helps shorten the harvesting period because of early maturation characteristics. The els1-1 allele with weakly impaired function of ELS1 has only a small effect on agricultural traits and could contribute to practical breeding.

Light Signaling-Dependent Regulation of PSII Biogenesis and Functional Maintenance

Light is a key environmental cue regulating photomorphogenesis and photosynthesis in plants. However, the molecular mechanisms underlying the interaction between light signaling pathways and photosystem function are unknown. Here, we show that various monochromatic wavelengths of light cooperate to regulate PSII function in Arabidopsis (Arabidopsis thaliana). The photoreceptors cryptochromes and phytochromes modulate the expression of HIGH CHLOROPHYLL FLUORESCENCE173 (HCF173), which is required for PSII biogenesis by regulating PSII core protein D1 synthesis mediated by the transcription factor ELONGATED HYPOCOTYL5 (HY5). HY5 directly binds to the ACGT-containing element ACE motif and G-box cis-element present in the HCF173 promoter and regulates its activity. PSII activity was decreased significantly in hy5 mutants under various monochromatic wavelengths of light. Interestingly, we demonstrate that HY5 also directly regulates the expression of the genes associated with PSII assembly and repair, including ALBINO3, HCF136, HYPERSENSITIVE TO HIGH LIGHT1, etc., which is required for the functional maintenance of PSII under photodamaging conditions. Moreover, deficiency of HY5 broadly decreases the accumulation of other photosystem proteins besides PSII proteins. Thus, our study reveals an important role of light signaling in both biogenesis and functional regulation of the photosystem and provides insight into the link between light signaling and photosynthesis in land plants.

EGY3: homologue of S2P protease located in chloroplasts

The EGY3 protein is a homologue of site-2 proteases, which are intramembrane zinc metalloproteases. EGY3 itself lacks proteolytic activity due to the absence of a zinc-binding motif. Plentiful evidence indicates that such intramembrane 'pseudoproteases' play significant roles in many diverse processes occurring within the cell. However, the physiological functions of EGY3, as well as its subcellular localization, remain unknown. The subcellular localization of EGY3 protein was investigated using Arabidopsis thaliana protoplasts transformed with EGY3-GFP fusion protein, and immunoblot experiments using the total leaf protein extract, as well as highly purified chloroplasts and fractions of stroma, envelope and thylakoid membrane proteins. The physiological role of EGY3 was studied using two A. thaliana mutant lines devoid of EGY3 protein. Chlorophyll a fluorescence measurement was performed and the egy3 mutant sensitivity to photoinhibition was investigated. Additionally, the abundance of thylakoid membrane complexes was established using blue native gel electrophoresis. We present experimental evidence for thylakoid membrane localization of the EGY3 protein. We show that egy3 mutants display increased value of the non-photochemical quenching parameter and significantly slower recovery rate after photoinhibitory treatment. This was associated with a decrease in the level of proteases involved in photosystem II recovery, Deg1 and FtsH2/8.

Copper-induced concomitant increases in photosynthesis, respiration, and C, N and S assimilation revealed by transcriptomic analyses in Ulva compressa (Chlorophyta)

BACKGROUND

The marine alga Ulva compressa is the dominant species in copper-polluted coastal areas in northern Chile. It has been shown that the alga tolerates micromolar concentrations of copper and accumulates copper at the intracellular level. Transcriptomic analyses were performed using total RNA of the alga cultivated with 10 μ M copper for 0, 1, 3 and 5 days using RNA-seq in order to identify processes involved in copper tolerance.

RESULTS

The levels of transcripts encoding proteins belonging to Light Harvesting Complex II (LHCII), photosystem II (PSII), cytochrome b6f, PSI, LHCI, ATP synthase and proteins involved in repair of PSII and protection of PSI were increased in the alga cultivated with copper. In addition, the level of transcripts encoding proteins of mitochondrial electron transport chain, ATP synthase, and enzymes involved in C, N and S assimilation were also enhanced. The higher percentages of increase in the level of transcripts were mainly observed at days 3 and 5. In contrast, transcripts involved protein synthesis and degradation, signal transduction, and replication and DNA repair, were decreased. In addition, net photosynthesis and respiration increased in the alga cultivated with copper, mainly at days 1 to 3. Furthermore, the activities of enzymes involved in C, N and S assimilation, rubisco, glutamine synthase and cysteine synthase, respectively, were also increased, mainly at days 1 and 3.

CONCLUSIONS

The marine alga U. compressa tolerates copper excess through a concomitant increase in expression of proteins involved in photosynthesis, respiration, and C, N and S assimilation, which represents an exceptional mechanism of copper tolerance.

Synergistic use of biochar and acidified manure for improving growth of maize in chromium contaminated soil

Chromium (Cr) contamination in farmlands has become a serious environmental concern due to the excessive use of industrial wastewater as an irrigation source. Therefore, some important measures need to be taken for reducing its mobility in a soil profile. A pot study was conducted to evaluate the effectiveness of sugarcane bagasse derived biochar and acidified manure on Cr mobility and its uptake by maize plant. Results showed that the application of biochar and acidified manure significantly changed soil pH, improved crop growth and as well as reduce the antioxidant response of maize in Cr contaminated soil. The concentration of bioavailable (AB-DTPA) extractable Cr in soil decreased with the addition of co-use of biochar (3%) and acidified manure (5%) by 36% relative to control. The maximum reduction in superoxidase dismutase (SOD), peroxidase dismutase (POD), and catalase activity assay (CAT), and ascorbate peroxidase activity (APX) was occurred by 41%, 51%, 20%, and 55%, respectively when biochar (3%) amended with the combination of acidified manure in Cr contaminated soil. Among all the amendments, biochar at 3% application combination with acidified manure (B2 + AMS) offered significantly minimize Cr mobility (Cr-III (44%) and Cr-VI (22%)) and thereby reduce its uptake by maize plant.

Barley cysteine protease PAP14 plays a role in degradation of chloroplast proteins

Chloroplast protein degradation is known to occur both inside chloroplasts and in the vacuole. Genes encoding cysteine proteases have been found to be highly expressed during leaf senescence. However, it remains unclear where they participate in chloroplast protein degradation. In this study HvPAP14, which belongs to the C1A family of cysteine proteases, was identified in senescing barley (Hordeum vulgare L.) leaves by affinity enrichment using the mechanism-based probe DCG-04 targeting cysteine proteases and subsequent mass spectrometry. Biochemical analyses and expression of a HvPAP14:RFP fusion construct in barley protoplasts was used to identify the subcellular localization and putative substrates of HvPAP14. The HvPAP14:RFP fusion protein was detected in the endoplasmic reticulum and in vesicular bodies. Immunological studies showed that HvPAP14 was mainly located in chloroplasts, where it was found in tight association with thylakoid membranes. The recombinant enzyme was activated by low pH, in accordance with the detection of HvPAP14 in the thylakoid lumen. Overexpression of HvPAP14 in barley revealed that the protease can cleave LHCB proteins and PSBO as well as the large subunit of Rubisco. HvPAP14 is involved in the normal turnover of chloroplast proteins and may have a function in bulk protein degradation during leaf senescence.

The zeaxanthin epoxidase is degraded along with the D1 protein during photoinhibition of photosystem II

The xanthophyll zeaxanthin is synthesized in chloroplasts upon high light exposure of plants and serves central photoprotective functions. The reconversion of zeaxanthin to violaxanthin is catalyzed by the zeaxanthin epoxidase (ZEP). ZEP shows highest activity after short and moderate high light periods, but becomes gradually down-regulated in response to increasing high light stress along with down-regulation of photosystem II (PSII) activity. ZEP activity and ZEP protein levels were studied in response to high light stress in four plant species: Arabidopsis thaliana, Pisum sativum, Nicotiana benthamiana and Spinacia oleracea. In all species, ZEP protein was degraded during photoinhibition of PSII in parallel with the D1 protein of PSII. In the presence of streptomycin, an inhibitor of chloroplast protein synthesis, photoinhibition of PSII and ZEP activity as well as degradation of D1 and ZEP protein was strongly increased, indicating a close correlation of ZEP regulation with PSII photoinhibition and repair. The concomitant high light-induced inactivation/degradation of ZEP and D1 prevents the reconversion of zeaxanthin during photoinhibition and repair of PSII. This regulation of ZEP activity supports a coordinated degradation of D1 and ZEP during photoinhibition/repair of PSII and an essential photoprotective function of zeaxanthin during the PSII repair cycle.

Dissecting Adaptation Mechanisms to Contrasting Solar Irradiance in the Mediterranean Shrub Cistus incanus

Molecular mechanisms that are the base of the strategies adopted by Mediterranean plants to cope with the challenges imposed by limited or excessive solar radiation during the summer season have received limited attention. In our study, conducted on C. incanus plants growing in the shade or in full sunlight, we performed measurements of relevant physiological traits, such as leaf water potential, gas exchange and PSII photochemistry, RNA-Seq with de-novo assembly, and the analysis of differentially expressed genes. We also identified and quantified photosynthetic pigments, abscisic acid, and flavonoids. Here, we show major mechanisms regulating light perception and signaling which, in turn, sustain the shade avoidance syndrome displayed by the 'sun loving' C. incanus. We offer clear evidence of the detrimental effects of excessive light on both the assembly and the stability of PSII, and the activation of a suite of both repair and effective antioxidant mechanisms in sun-adapted leaves. For instance, our study supports the view of major antioxidant functions of zeaxanthin in sunny plants concomitantly challenged by severe drought stress. Finally, our study confirms the multiple functions served by flavonoids, both flavonols and flavanols, in the adaptive mechanisms of plants to the environmental pressures associated to Mediterranean climate.

Photoinhibition of Photosystem I Provides Oxidative Protection During Imbalanced Photosynthetic Electron Transport in Arabidopsis thaliana

Photosynthesis involves the conversion of sunlight energy into stored chemical energy, which is achieved through electron transport along a series of redox reactions. Excess photosynthetic electron transport might be dangerous due to the risk of molecular oxygen reduction, generating reactive oxygen species (ROS) over-accumulation. Avoiding excess ROS production requires the rate of electron transport to be coordinated with the capacity of electron acceptors in the chloroplast stroma. Imbalance between the donor and acceptor sides of photosystem I (PSI) can lead to inactivation, which is called PSI photoinhibition. We used a light-inducible PSI photoinhibition system in Arabidopsis thaliana to resolve the time dynamics of inhibition and to investigate its impact on ROS production and turnover. The oxidation state of the PSI reaction center and rates of CO2 fixation both indicated strong and rapid PSI photoinhibition upon donor side/acceptor side imbalance, while the rate of inhibition eased during prolonged imbalance. PSI photoinhibition was not associated with any major changes in ROS accumulation or antioxidant activity; however, a lower level of lipid oxidation correlated with lower abundance of chloroplast lipoxygenase in PSI-inhibited leaves. The results of this study suggest that rapid activation of PSI photoinhibition under severe photosynthetic imbalance protects the chloroplast from over-reduction and excess ROS formation.

The potential of quantitative models to improve microalgae photosynthetic efficiency

The massive increase in carbon dioxide concentration in the atmosphere driven by human activities is causing huge negative consequences and new sustainable sources of energy, food and materials are highly needed. Algae are unicellular photosynthetic microorganisms that can provide a highly strategic contribution to this challenge as alternative source of biomass to complement crops cultivation. Algae industrial cultures are commonly limited by light availability, and biomass accumulation is strongly dependent on their photon-to-biomass conversion efficiency. Investigation of algae photosynthetic metabolism is thus strategic for the generation of more efficient strains with higher productivity. Algae are cultivated at industrial scale in conditions highly different from the natural niches they adapted to and strains development efforts must fully consider the seminal influence on productivity of regulatory mechanism of photosynthesis as well as of cultivation parameters like cells concentration, light distribution in the culture, mixing, nutrients and carbon dioxide availability. In this review we will focus in particular on how mathematical models can account for the complex influence of all environmental parameters and can be exploited for development of improved algae strains.

Reduced expression of the proteolytically inactive FtsH members has impacts on the Darwinian fitness of Arabidopsis thaliana

FtsH (filamentation-temperature-sensitive protein H) proteases are a family of membrane-bound enzymes present in eubacteria, animals, and plants. Besides the 12 genes encoding proteolytically active members of the FtsH family in the genome of Arabidopsis, there are five genes coding for members that are assumed to be proteolytically inactive due to mutations in the protease domain; these are termed FtsHi (i for inactive). Despite their lack of proteolytic activity, these FtsHi members seem to be important for chloroplast and plant development as four out of five homozygous knockout-mutants of FtsHis are embryo-lethal. Here, we analysed the Darwinian fitness of weak homozygous (ftshi1,3,4) and heterozygous (ftshi/FTSHi2,4,5) mutants. We compared the growth and development of these mutants to their respective wild-type Arabidopsis plants under controlled laboratory conditions and in the field, and we also evaluated the photosynthetic efficiency by pulse-amplitude modulation fluorescence. Homologous genotypes were subjected to various stress conditions in a greenhouse and gene co-expression as well as phylogenetic analyses were performed. Analysis of the gene-expression network of the five FTSHi genes indicated common clusters with genes encoding FtsH12, OTP51, and methylase. Phylogenetic analyses pointed to a common evolution (and common disappearance in grasses and gymnosperms) of FtsH12 and multiple presumably proteolytically inactive FtsHi enzymes. Our data show that the FtsHi enzymes are highly important during the seedling stage and for Darwinian fitness analyses in semi-natural conditions.

Chlorophyll catabolism precedes changes in chloroplast structure and proteome during leaf senescence

The earliest visual changes of leaf senescence occur in the chloroplast as chlorophyll is degraded and photosynthesis declines. Yet, a comprehensive understanding of the sequence of catabolic events occurring in chloroplasts during natural leaf senescence is still missing. Here, we combined confocal and electron microscopy together with proteomics and biochemistry to follow structural and molecular changes during Arabidopsis leaf senescence. We observed that initiation of chlorophyll catabolism precedes other breakdown processes. Chloroplast size, stacking of thylakoids, and efficiency of PSII remain stable until late stages of senescence, whereas the number and size of plastoglobules increase. Unlike catabolic enzymes, whose level increase, the level of most proteins decreases during senescence, and chloroplast proteins are overrepresented among these. However, the rate of their disappearance is variable, mostly uncoordinated and independent of their inherent stability during earlier developmental stages. Unexpectedly, degradation of chlorophyll-binding proteins lags behind chlorophyll catabolism. Autophagy and vacuole proteins are retained at relatively high levels, highlighting the role of extra-plastidic degradation processes especially in late stages of senescence. The observation that chlorophyll catabolism precedes all other catabolic events may suggest that this process enables or signals further catabolic processes in chloroplasts.

Phosphorylation of the Chloroplastic Metalloprotease FtsH in Arabidopsis Characterized by Phos-Tag SDS-PAGE

FtsH is an essential ATP-dependent metalloprotease for protein quality control in the thylakoid membrane of Arabidopsis thaliana chloroplasts. It is required for chloroplast development during leaf growth, and particularly for the specific degradation of photo-damaged D1 protein in the photosystem II (PSII) complex to maintain photosynthesis activity. In the thylakoid membrane, the reversible phosphorylation of proteins is known to control the activity and remodeling of photosynthetic complexes, and previous studies implicate that FtsH is also phosphorylated. We therefore assessed the phosphorylation status of FtsH and its possible role in the regulatory mechanism in this study. The phosphorylation level of FtsHs that compose the FtsH heterohexameric complex was investigated by phosphate-affinity gel electrophoresis using a Phos-Tag molecule. Phos-tag SDS-PAGE of thylakoid proteins and subsequent immunoblot analysis showed that both type A (FtsH1/5) and type B (FtsH2/8) subunits were separable into phosphorylated and non-phosphorylated forms. Neither different light conditions nor the lack of two major thylakoid kinases, STN7 and STN8, resulted in any clear difference in FtsH phosphorylation, suggesting that this process is independent of the light-dependent regulation of photosynthesis-related proteins. Site-directed mutagenesis of putatively phosphorylated Ser or Thr residues into Ala demonstrated that Ser-212 may play a role in FtsH stability in the thylakoid membranes. Different phosphorylation status of FtsH oligomers analyzed by two-dimensional clear-native/Phos-tag SDS-PAGE implied that phosphorylation partially affects FtsH complex formation or its stability.

A New Light on Photosystem II Maintenance in Oxygenic Photosynthesis

Life on earth is sustained by oxygenic photosynthesis, a process that converts solar energy, carbon dioxide, and water into chemical energy and biomass. Sunlight is essential for growth and productivity of photosynthetic organisms. However, exposure to an excessive amount of light adversely affects fitness due to photooxidative damage to the photosynthetic machinery, primarily to the reaction center of the oxygen-evolving photosystem II (PSII). Photosynthetic organisms have evolved diverse photoprotective and adaptive strategies to avoid, alleviate, and repair PSII damage caused by high-irradiance or fluctuating light. Rapid and harmless dissipation of excess absorbed light within antenna as heat, which is measured by chlorophyll fluorescence as non-photochemical quenching (NPQ), constitutes one of the most efficient protective strategies. In parallel, an elaborate repair system represents another efficient strategy to maintain PSII reaction centers in active states. This article reviews both the reaction center-based strategy for robust repair of photodamaged PSII and the antenna-based strategy for swift control of PSII light-harvesting (NPQ). We discuss evolutionarily and mechanistically diverse strategies used by photosynthetic organisms to maintain PSII function for growth and productivity under static high-irradiance light or fluctuating light environments. Knowledge of mechanisms underlying PSII maintenance would facilitate bioengineering photosynthesis to enhance agricultural productivity and sustainability to feed a growing world population amidst climate change.

Exogenous Melatonin Alleviates Oxidative Damages and Protects Photosystem II in Maize Seedlings Under Drought Stress

The protective role of melatonin in plants against various abiotic stresses have been widely demonstrated, but poorly explored in organ-specific responses and the transmission of melatonin signals across organs. In this study, the effects of melatonin with the root-irrigation method and the leaf-spraying method on the antioxidant system and photosynthetic machinery in maize seedlings under drought stress were investigated. The results showed that drought stress led to the rise in reactive oxygen species (ROS), severe cell death, and degradation of D1 protein, which were mitigated by the melatonin application. The application of melatonin improved the photosynthetic activities and alleviated the oxidative damages of maize seedlings under the drought stress. Compared with the leaf-spraying method, the root-irrigation method was more effective on enhancing drought tolerance. Moreover, maize seedlings made organ-specific physiological responses to the drought stress, and the physiological effects of melatonin varied with the dosage, application methods and plant organs. The signals of exogenous melatonin received by roots could affect the stress responses of leaves, and the melatonin signals perceived by leaves also led to changes in physiological metabolisms in roots under the stress. Consequently, the whole seedlings coordinated the different parts and made a systemic acclimation against the drought stress. Melatonin as a protective agent against abiotic stresses has a potential application prospect in the agricultural industry.

Heterologous synthesis of chlorophyll b in Nannochloropsis salina enhances growth and lipid production by increasing photosynthetic efficiency

BACKGROUND

Chlorophylls play important roles in photosynthesis, and thus are critical for growth and related metabolic pathways in photosynthetic organisms. They are particularly important in microalgae, emerging as the next generation feedstock for biomass and biofuels. Nannochloropsis are industrial microalgae for these purposes, but are peculiar in that they lack accessory chlorophylls. In addition, the localization of heterologous proteins to the chloroplast of Nannochloropsis has not been fully studied, due to the secondary plastid surrounded by four membranes. This study addressed questions of correct localization and functional benefits of heterologous expression of chlorophyllide a oxygenase from Chlamydomonas (CrCAO) in Nannochloropsis.

RESULTS

We cloned CrCAO from Chlamydomonas, which catalyzes oxidation of Chla producing Chlb, and overexpressed it in N. salina to reveal effects of the heterologous Chlb for photosynthesis, growth, and lipid production. For correct localization of CrCAO into the secondary plastid in N. salina, we added the signal-recognition sequence and the transit peptide (cloned from an endogenous chloroplast-localized protein) to the N terminus of CrCAO. We obtained two transformants that expressed CrCAO and produced Chlb. They showed improved growth under medium light (90 μmol/m²/s) conditions, and their photosynthetic efficiency was increased compared to WT. They also showed increased expression of certain photosynthetic proteins, accompanied by an increased maximum electron-transfer rate up to 15.8% and quantum yields up to 17%, likely supporting the faster growth. This improved growth resulted in increased biomass production, and more importantly lipid productivity particularly with medium light.

CONCLUSIONS

We demonstrated beneficial effects of heterologous expression of CrCAO in Chlb-less organism N. salina, where the newly produced Chlb enhanced photosynthesis and growth. Accordingly, transformants showed improved production of biomass and lipids, important traits of microalgae from the industrial perspectives. Our transformants are the first Nannochloropsis cells that produced Chlb in the whole evolutionary path. We also succeeded in delivering a heterologous protein into the secondary plastid for the first time in Nannochloropsis. Taken together, our data showed that manipulation of photosynthetic pigments, including Chlb, can be employed in genetic improvements of microalgae for production of biofuels and other biomaterials.

The Chloroplast Envelope Protease FTSH11 - Interaction With CPN60 and Identification of Potential Substrates

FTSH proteases are membrane-bound, ATP-dependent metalloproteases found in bacteria, mitochondria and chloroplasts. The product of one of the 12 genes encoding FTSH proteases in Arabidopsis, FTSH11, has been previously shown to be essential for acquired thermotolerance. However, the substrates of this protease, as well as the mechanism linking it to thermotolerance are largely unknown. To get insight into these, the FTSH11 knockout mutant was complemented with proteolytically active or inactive variants of this protease, tagged with HA-tag, under the control of the native promoter. Using these plants in thermotolerance assay demonstrated that the proteolytic activity, and not only the ATPase one, is essential for conferring thermotolerance. Immunoblot analyses of leaf extracts, isolated organelles and sub-fractionated chloroplast membranes localized FTSH11 mostly to chloroplast envelopes. Affinity purification followed by mass spectrometry analysis revealed interaction between FTSH11 and different components of the CPN60 chaperonin. In affinity enrichment assays, CPN60s as well as a number of envelope, stroma and thylakoid proteins were found associated with proteolytically inactive FTSH11. Comparative proteomic analysis of WT and knockout plants, grown at 20°C or exposed to 30°C for 6 h, revealed a plethora of upregulated chloroplast proteins in the knockout, some of them might be candidate substrates. Among these stood out TIC40, which was stabilized in the knockout line after recovery from heat stress, and three proteins that were found trapped in the affinity enrichment assay: the nucleotide antiporter PAPST2, the fatty acid binding protein FAP1 and the chaperone HSP70. The consistent behavior of these four proteins in different assays suggest that they are potential FTSH11 substrates.

Impairment of FtsHi5 Function Affects Cellular Redox Balance and Photorespiratory Metabolism in Arabidopsis

Photorespiration is an essential process for plant photosynthesis, development and growth in aerobic conditions. Recent studies have shown that photorespiration is an open system integrated with the plant primary metabolism network and intracellular redox systems, though the mechanisms of regulating photorespiration are far from clear. Through a forward genetic method, we identified a photorespiratory mutant pr1 (photorespiratory related 1), which produced a chlorotic and smaller photorespiratory growth phenotype with decreased chlorophyll content and accumulation of glycine and serine in ambient air. Morphological and physiological defects in pr1 plants can be largely abolished under elevated CO2 conditions. Genetic mapping and complementation confirmed that PR1 encodes an FtsH (Filamentation temperature-sensitive H)-like protein, FtsHi5. Reduced FtsHi5 expression in DEX-induced RNAi transgenic plants produced a similar growth phenotype with pr1 (ftsHi5-1). Transcriptome analysis suggested a changed expression pattern of redox-related genes and an increased expression of senescence-related genes in DEX: RNAi-FtsHi5 seedlings. Together with the observation that decreased accumulation of D1 and D2 proteins of photosystem II (PSII) and over-accumulation of reactive oxygen species (ROS) in ftsHi5 mutants, we hypothesize that FtsHi5 functions in maintaining the cellular redox balance and thus regulates photorespiratory metabolism.