A linker protein from a red-type pyrenoid phase separates with Rubisco via oligomerizing sticker motifs.

The slow kinetics and poor substrate specificity of the key photosynthetic CO2-fixing enzyme Rubisco have prompted the repeated evolution of Rubisco-containing biomolecular condensates known as pyrenoids in the majority of eukaryotic microalgae. Diatoms dominate marine photosynthesis, but the interactions underlying their pyrenoids are unknown. Here, we identify and characterize the Rubisco linker protein PYCO1 from Phaeodactylum tricornutum. PYCO1 is a tandem repeat protein containing prion-like domains that localizes to the pyrenoid. It undergoes homotypic liquid-liquid phase separation (LLPS) to form condensates that specifically partition diatom Rubisco. Saturation of PYCO1 condensates with Rubisco greatly reduces the mobility of droplet components. Cryo-electron microscopy and mutagenesis data revealed the sticker motifs required for homotypic and heterotypic phase separation. Our data indicate that the PYCO1-Rubisco network is cross-linked by PYCO1 stickers that oligomerize to bind to the small subunits lining the central solvent channel of the Rubisco holoenzyme. A second sticker motif binds to the large subunit. Pyrenoidal Rubisco condensates are highly diverse and tractable models of functional LLPS.

The structural basis of Rubisco phase separation in the pyrenoid.

Approximately one-third of global CO2 fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO2-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle.

Biomolecular condensates in photosynthesis and metabolism.

The transient assembly or sequestration of enzymes into clusters permits the channeling of metabolites, but requires spatiotemporal control. Liquid liquid phase separation (LLPS) has recently emerged as a fundamental concept enabling formation of such assemblies into non-membrane bound organelles. The role of LLPS in the formation of condensates containing the CO2-fixing enzyme Rubisco has recently become appreciated. Both prokaryotic carboxysomes and eukaryotic pyrenoids enhance the carboxylation reaction by enabling the saturation of the enzyme with CO2 gas. Biochemical reconstitution and structural biology are revealing the mechanistic basis of these photosynthetic condensates. At the same time other enzyme clusters, such as purinosomes for de-novo purine biosynthesis and G-bodies containing glycolytic enzymes, are emerging to behave like phase-separated systems. In the near future we anticipate details of many more such metabolic condensates to be revealed, deeply informing our ability to influence metabolic fluxes.

The pyrenoidal linker protein EPYC1 phase separates with hybrid Arabidopsis-Chlamydomonas Rubisco through interactions with the algal Rubisco small subunit.

Photosynthetic efficiencies in plants are restricted by the CO2-fixing enzyme Rubisco but could be enhanced by introducing a CO2-concentrating mechanism (CCM) from green algae, such as Chlamydomonas reinhardtii (hereafter Chlamydomonas). A key feature of the algal CCM is aggregation of Rubisco in the pyrenoid, a liquid-like organelle in the chloroplast. Here we have used a yeast two-hybrid system and higher plants to investigate the protein-protein interaction between Rubisco and essential pyrenoid component 1 (EPYC1), a linker protein required for Rubisco aggregation. We showed that EPYC1 interacts with the small subunit of Rubisco (SSU) from Chlamydomonas and that EPYC1 has at least five SSU interaction sites. Interaction is crucially dependent on the two surface-exposed α-helices of the Chlamydomonas SSU. EPYC1 could be localized to the chloroplast in higher plants and was not detrimental to growth when expressed stably in Arabidopsis with or without a Chlamydomonas SSU. Although EPYC1 interacted with Rubisco in planta, EPYC1 was a target for proteolytic degradation. Plants expressing EPYC1 did not show obvious evidence of Rubisco aggregation. Nevertheless, hybrid Arabidopsis Rubisco containing the Chlamydomonas SSU could phase separate into liquid droplets with purified EPYC1 in vitro, providing the first evidence of pyrenoid-like aggregation for Rubisco derived from a higher plant.

CO2 -fixing liquid droplets: Towards a dissection of the microalgal pyrenoid.

CO2 enters the biosphere via the slow, oxygen-sensitive carboxylase, Rubisco. To compensate, most microalgae saturate Rubisco with its substrate gas through a carbon dioxide concentrating mechanism. This strategy frequently involves compartmentalization of the enzyme in the pyrenoid, a non-membrane enclosed compartment of the chloroplast stroma. Recently, tremendous advances have been achieved concerning the structure, physical properties, composition and in vitro reconstitution of the pyrenoid matrix from the green alga Chlamydomonas reinhardtii. The discovery of the intrinsically disordered multivalent Rubisco linker protein EPYC1 provided a biochemical framework to explain the subsequent finding that the pyrenoid resembles a liquid droplet in vivo. Reconstitution of the corresponding liquid-liquid phase separation using pure Rubisco and EPYC1 allowed a detailed characterization of this process. Finally, a large high-quality dataset of pyrenoidal protein-protein interactions inclusive of spatial information provides ample substrate for rapid further functional dissection of the pyrenoid. Integrating and extending recent advances will inform synthetic biology efforts towards enhancing plant photosynthesis as well as contribute a versatile model towards experimentally dissecting the biochemistry of enzyme-containing membraneless organelles.

The phase separation underlying the pyrenoid-based microalgal Rubisco supercharger.

The slow and promiscuous properties of the CO2-fixing enzyme Rubisco constrain photosynthetic efficiency and have prompted the evolution of powerful CO2 concentrating mechanisms (CCMs). In eukaryotic microalgae a key strategy involves sequestration of the enzyme in the pyrenoid, a liquid non-membranous compartment of the chloroplast stroma. Here we show using pure components that two proteins, Rubisco and the linker protein Essential Pyrenoid Component 1 (EPYC1), are both necessary and sufficient to phase separate and form liquid droplets. The phase-separated Rubisco is functional. Droplet composition is dynamic and components rapidly exchange with the bulk solution. Heterologous and chimeric Rubiscos exhibit variability in their tendency to demix with EPYC1. The ability to dissect aspects of pyrenoid biochemistry in vitro will permit us to inform and guide synthetic biology ambitions aiming to engineer microalgal CCMs into crop plants.

Structural insights into the LCIB protein family reveals a new group of ß-carbonic anhydrases.

Aquatic microalgae have evolved diverse CO2-concentrating mechanisms (CCMs) to saturate the carboxylase with its substrate, to compensate for the slow kinetics and competing oxygenation reaction of the key photosynthetic CO2-fixing enzyme rubisco. The limiting CO2-inducible B protein (LCIB) is known to be essential for CCM function in Chlamydomonas reinhardtii To assign a function to this previously uncharacterized protein family, we purified and characterized a phylogenetically diverse set of LCIB homologs. Three of the six homologs are functional carbonic anhydrases (CAs). We determined the crystal structures of LCIB and limiting CO2-inducible C protein (LCIC) from C. reinhardtii and a CA-functional homolog from Phaeodactylum tricornutum, all of which harbor motifs bearing close resemblance to the active site of canonical ß-CAs. Our results identify the LCIB family as a previously unidentified group of ß-CAs, and provide a biochemical foundation for their function in the microalgal CCMs.

The major thylakoid protein kinases STN7 and STN8 revisited: effects of altered STN8 levels and regulatory specificities of the STN kinases.

Thylakoid phosphorylation is predominantly mediated by the protein kinases STN7 and STN8. While STN7 primarily catalyzes LHCII phosphorylation, which enables LHCII to migrate from photosystem (PS) II to PSI, STN8 mainly phosphorylates PSII core proteins. The reversible phosphorylation of PSII core proteins is thought to regulate the PSII repair cycle and PSII supercomplex stability, and play a role in modulating the folding of thylakoid membranes. Earlier studies clearly demonstrated a considerable substrate overlap between the two STN kinases, raising the possibility of a balanced interdependence between them at either the protein or activity level. Here, we show that such an interdependence of the STN kinases on protein level does not seem to exist as neither knock-out nor overexpression of STN7 or STN8 affects accumulation of the other. STN7 and STN8 are both shown to be integral thylakoid proteins that form part of molecular supercomplexes, but exhibit different spatial distributions and are subject to different modes of regulation. Evidence is presented for the existence of a second redox-sensitive motif in STN7, which seems to be targeted by thioredoxin f. Effects of altered STN8 levels on PSII core phosphorylation, supercomplex formation, photosynthetic performance and thylakoid ultrastructure were analyzed in Arabidopsis thaliana using STN8-overexpressing plants (oeSTN8). In general, oeSTN8 plants were less sensitive to intense light and exhibited changes in thylakoid ultrastructure, with grana stacks containing more layers and reduced amounts of PSII supercomplexes. Hence, we conclude that STN8 acts in an amount-dependent manner similar to what was shown for STN7 in previous studies. However, the modes of regulation of the STN kinases appear to differ significantly.

PGRL1 is the elusive ferredoxin-plastoquinone reductase in photosynthetic cyclic electron flow.

During plant photosynthesis, photosystems I (PSI) and II (PSII), located in the thylakoid membranes of the chloroplast, use light energy to mobilize electron transport. Different modes of electron flow exist. Linear electron flow is driven by both photosystems and generates ATP and NADPH, whereas cyclic electron flow (CEF) is driven by PSI alone and generates ATP only. Two variants of CEF exist in flowering plants, of which one is sensitive to antimycin A (AA) and involves the two thylakoid proteins, PGR5 and PGRL1. However, neither the mechanism nor the site of reinjection of electrons from ferredoxin into the thylakoid electron transport chain during AA-sensitive CEF is known. Here, we show that PGRL1 accepts electrons from ferredoxin in a PGR5-dependent manner and reduces quinones in an AA-sensitive fashion. PGRL1 activity itself requires several redox-active cysteine residues and a Fe-containing cofactor. We therefore propose that PGRL1 is the elusive ferredoxin-plastoquinone reductase (FQR).

Control of STN7 transcript abundance and transient STN7 dimerisation are involved in the regulation of STN7 activity.

Reversible phosphorylation of LHCII, the light-harvesting complex of photosystem II, controls its migration between the two photosystems (state transitions), and serves to adapt the photosynthetic machinery of plants and green algae to short-term changes in ambient light conditions. The thylakoid kinase STN7 is required for LHCII phosphorylation and state transitions in vascular plants. Regulation of STN7 levels occurs at the post-translational level, depends on the thylakoid redox state, and might involve reversible autophosphorylation. Here, we have analysed the effects of different light conditions and chemical inhibitors on the abundance of STN7 transcripts and their products. This analysis was performed in wild-type Arabidopsis thaliana plants, in several photosynthetic mutants, and in lines overexpressing STN7 (oeSTN7) or expressing mutant variants of STN7 carrying single or double cysteine-serine exchanges. It was found that accumulation of the STN7 protein is also controlled at the level of transcript abundance. Under certain conditions, exposure to high light or far-red light treatment, the relative decreases in LHCII phosphorylation can be attributed to decreases in STN7 abundance. Nevertheless, inhibitor experiments showed that redox control of LHCII kinase activity persists in oeSTN7 plants. STN7 dimers were found in oeSTN7 plants and in lines with single cysteine-serine exchanges, indicating that dimerisation involves disulphide bridges. We speculate that transient STN7 dimerisation is required for STN7 activity, and that the altered dimerisation behaviour of oeSTN7 plants might be responsible for the unusually high phosphorylation of LHCII in the dark found in this genotype.

Dynamics of reversible protein phosphorylation in thylakoids of flowering plants: the roles of STN7, STN8 and TAP38.

Phosphorylation is the most common post-translational modification found in thylakoid membrane proteins of flowering plants, targeting more than two dozen subunits of all multiprotein complexes, including some light-harvesting proteins. Recent progress in mass spectrometry-based technologies has led to the detection of novel low-abundance thylakoid phosphoproteins and localised their phosphorylation sites. Three of the enzymes involved in phosphorylation/dephosphorylation cycles in thylakoids, the protein kinases STN7 and STN8 and the phosphatase TAP38/PPH1, have been characterised in the model species Arabidopsis thaliana. Differential protein phosphorylation is associated with changes in illumination and various other environmental parameters, and has been implicated in several acclimation responses, the molecular mechanisms of which are only partly understood. The phenomenon of State Transitions, which enables rapid adaptation to short-term changes in illumination, has recently been shown to depend on reversible phosphorylation of LHCII by STN7-TAP38/PPH1. STN7 is also necessary for long-term acclimation responses that counteract imbalances in energy distribution between PSII and PSI by changing the rates of accumulation of their reaction-centre and light-harvesting proteins. Another aspect of photosynthetic acclimation, the modulation of thylakoid ultrastructure, depends on phosphorylation of PSII core proteins, mainly executed by STN8. Here we review recent advances in the characterisation of STN7, STN8 and TAP38/PPH1, and discuss their physiological significance within the overall network of thylakoid protein phosphorylation. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.

The invariant phenylalanine of precursor proteins discloses the importance of Omp85 for protein translocation into cyanelles.

BACKGROUND: Today it is widely accepted that plastids are of cyanobacterial origin. During their evolutionary integration into the metabolic and regulatory networks of the host cell the engulfed cyanobacteria lost their independency. This process was paralleled by a massive gene transfer from symbiont to the host nucleus challenging the development of a retrograde protein translocation system to ensure plastid functionality. Such a system includes specific targeting signals of the proteins needed for the function of the plastid and membrane-bound machineries performing the transfer of these proteins across the envelope membranes. At present, most information on protein translocation is obtained by the analysis of land plants. However, the analysis of protein import into the primitive plastids of glaucocystophyte algae, revealed distinct features placing this system as a tool to understand the evolutionary development of translocation systems. Here, bacterial outer membrane proteins of the Omp85 family have recently been discussed as evolutionary seeds for the development of translocation systems. RESULTS: To further explore the initial mode of protein translocation, the observed phenylalanine dependence for protein translocation into glaucophyte plastids was pursued in detail. We document that indeed the phenylalanine has an impact on both, lipid binding and binding to proteoliposomes hosting an Omp85 homologue. Comparison to established import experiments, however, unveiled a major importance of the phenylalanine for recognition by Omp85. This finding is placed into the context of the evolutionary development of the plastid translocon. CONCLUSION: The phenylalanine in the N-terminal domain signs as a prerequisite for protein translocation across the outer membrane assisted by a "primitive" translocon. This amino acid appears to be optimized for specifically targeting the Omp85 protein without enforcing aggregation on the membrane surface. The phenylalanine has subsequently been lost in the transit sequence, but can be found at the C-terminal position of the translocating pore. Thereby, the current hypothesis of Omp85 being the prokaryotic contribution to the ancestral Toc translocon can be supported.