A phase-separated CO2-fixing pyrenoid proteome determined by TurboID in Chlamydomonas reinhardtii

The thylakoid- and pyrenoid-localized phosphate transporter PHT4-9 is essential for photosynthesis in Chlamydomonas

Phosphate (Pi) is essential for photosynthesis in the chloroplast of algae and plants. Pi homeostasis in the chloroplast is maintained by transporters from several families, whose identities in algae are largely unknown as compared with land plants. Here, we assess the role of the putative PHOSPHATE TRANSPORTER 4-9 from Chlamydomonas reinhardtii (CrPHT4-9) in maintaining chloroplast Pi homeostasis and modulating photosynthesis. Based on phylogenetic analyses and heterologous expression in a yeast (Saccharomyces cerevisiae) strain lacking Pi transporters, we demonstrate that CrPHT4-9 is a Pi transporter closely related to the chloroplast members of the PHT4 family in Arabidopsis (Arabidopsis thaliana). CrPHT4-9 is localized within the chloroplast, more specifically in the thylakoid membrane network and the tubules traversing the CO2-fixing pyrenoid. Two mutants lacking CrPHT4-9 (Crpht4-9) exhibit defective photoautotrophic growth, altered cell morphology and chloroplast ultrastructure under CO2-limiting conditions. In the Crpht4-9 mutants, we further show an increased proton motive force across the thylakoid membrane, enhanced energy- and state-transition-dependent non-photochemical quenching of chlorophyll a fluorescence, and diminished photosynthetic electron transport and ATP synthase activity. The Crpht4-9 mutants exhibit reduced affinity to inorganic carbon, indicating an impaired carbon-concentrating mechanism. These phenotypes are largely recovered by genetic complementation as well as by ample CO2 supply and, interestingly, by Pi deprivation. Therefore, we conclude that the thylakoid- and pyrenoid-localized CrPHT4-9 maintains Pi homeostasis within the chloroplast and is essential for photosynthesis and growth.

Synthetic biology approaches to improve Rubisco carboxylation efficiency in C3 Plants: Direct and Indirect Strategies

Food security remains a pressing issue due to the growing global population and climate change, including the global warming along with increased atmospheric CO2 levels, which can negatively impact C3 crop yields. A major limitation in C3 plants is the inefficiency of Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) due to its low carboxylation activity and competing oxygenase activity. Improving Rubisco efficiency in C3 plants is thus essential for improving photosynthetic performance. Recent advances in synthetic biology have introduced promising strategies to overcome these limitations. This review highlights the latest synthetic biology and gene transformation techniques aimed at optimizing Rubsico carboxylation efficiency. Next, direct approaches such as engineering Rubisco subunits by replacing plant Rubisco with proteins from other organisms are discussed. Additionally, indirect strategies involve modifications of Rubisco-interacting proteins and adjustment of Rubisco environment. We explore CO2-concentrating mechanisms (CCMs) based on pyrenoids and carboxysomes, which increase local CO2 concentrations around Rubisco thus favouring the carboxylation reaction. Lastly, photorespiratory bypasses are also covered in this review.

From algae to plants: understanding pyrenoid-based CO2-concentrating mechanisms

Pyrenoids are the key component of one of the most abundant biological CO2 concentration mechanisms found in nature. Pyrenoid-based CO2-concentrating mechanisms (pCCMs) are estimated to account for one third of global photosynthetic CO2 capture. Our molecular understanding of how pyrenoids work is based largely on work in the green algae Chlamydomonas reinhardtii. Here, we review recent advances in our fundamental knowledge of the biogenesis, architecture, and function of pyrenoids in Chlamydomonas and ongoing engineering biology efforts to introduce a functional pCCM into chloroplasts of vascular plants, which, if successful, has the potential to enhance crop productivity and resilience to climate change.

A sensitive and reliable method for the quantitative determination of hydrogen peroxide produced by microalgae cells

One of the reactive forms of oxygen is hydrogen peroxide (H2O2), which has been investigated as a key component of growth processes and stress responses. Different methods for the determination of H2O2 production by animal and bacterial cells exist; however, its detection in algal cell cultures is more complicated due to the presence of photosynthetic pigments in the cells and the complex structure of cell walls. Considering these issues, a reliable, quick, and simple method for H2O2 detection is needed in phycological research. The aim of this methodological study was to optimize an Amplex UltraRed method for the fluorometric detection of H2O2 produced by microalgae cells, using a wild-type strain of Chlamydomonas reinhardtii as a model. The results showed that (i) potassium phosphate is the most suitable reaction buffer for this method, (ii) a 560 nm wavelength variant is the most appropriate as the excitation wavelength for fluorescence spectra measurement, (iii) a 50:50 ratio for the reaction mixture to sample was the most suitable, (iv) the fluorescence signal was significantly influenced by the density of the microalgae biomass, and (v) sample fortification with H2O2 allowed for an increase of the method's reliability and repeatability. The proposed protocol of the Amplex UltraRed method for the fluorometric detection of H2O2 produced by microalgae cells can yield a sensitive and accurate determination of the content of the test compound, minimizing measurement errors, eliminating chlorophyll autofluorescence problem, and compensating for the matrix effect. This method can be applied to the study of other microalgae species.

Proteomic analysis of the pyrenoid-traversing membranes of Chlamydomonas reinhardtii reveals novel components

Pyrenoids are algal CO2-fixing organelles that mediate approximately one-third of global carbon fixation and hold the potential to enhance crop growth if engineered into land plants. Most pyrenoids are traversed by membranes that are thought to supply them with concentrated CO2. Despite the critical nature of these membranes for pyrenoid function, they are poorly understood, with few protein components known in any species.• Here we identify protein components of the pyrenoid-traversing membranes from the leading model alga Chlamydomonas reinhardtii by affinity purification and mass spectrometry of membrane fragments. Our proteome includes previously-known proteins as well as novel candidates.• We further characterize two of the novel pyrenoid-traversing membrane-resident proteins, Cre10.g452250, which we name Pyrenoid Membrane Enriched 1 (PME1), and LCI16. We confirm their localization, observe that they physically interact, and find that neither protein is required for normal membrane morphology.• Taken together, our study identifies the proteome of pyrenoid-traversing membranes and initiates the characterization of a novel pyrenoid-traversing membrane complex, building toward a mechanistic understanding of the pyrenoid.

A protein blueprint of the diatom CO2-fixing organelle

Diatoms are central to the global carbon cycle. At the heart of diatom carbon fixation is an overlooked organelle called the pyrenoid, where concentrated CO2 is delivered to densely packed Rubisco. Diatom pyrenoids fix approximately one-fifth of global CO2, but the protein composition of this organelle is largely unknown. Using fluorescence protein tagging and affinity purification-mass spectrometry, we generate a high-confidence spatially defined protein-protein interaction network for the diatom pyrenoid. Within our pyrenoid interaction network are 10 proteins with previously unknown functions. We show that six of these form a shell that encapsulates the Rubisco matrix and is critical for pyrenoid structural integrity, shape, and function. Although not conserved at a sequence or structural level, the diatom pyrenoid shares some architectural similarities to prokaryotic carboxysomes. Collectively, our results support the convergent evolution of pyrenoids across the two main plastid lineages and uncover a major structural and functional component of global CO2 fixation.

Stress induced factor 2 is a dual regulator for defense and seed germination in Arabidopsis

Receptor-like kinases (RLKs) constitute a diverse superfamily of proteins pivotal for various plant physiological processes, including responses to pathogens, hormone perception, growth, and development. Their ability to recognize conserved epitopes for general elicitors and specific pathogens marked significant advancements in plant pathology research. Emerging evidence suggests that RLKs and associated components also act as modulators in hormone signaling and cellular trafficking, showcasing their multifunctional roles in growth and development. Notably, STRESS INDUCED FACTOR 2 (SIF2) stands out as a representative with distinct expression patterns in different Arabidopsis organs. Our prior work highlighted the specific induction of SIF2 expression in guard cells, emphasizing its positive contribution to stomatal immunity. Expanding on these findings, our present study delves into the diverse functions of SIF2 expression in root tissues. Utilizing comprehensive physiology, molecular biology, protein biochemistry, and genetic analyses, we reveal that SIF2 modulates abscisic acid (ABA) signaling in Arabidopsis roots. SIF2 is epistatic with key regulators in the ABA signaling pathway, thereby governing the expression of genes crucial for dormancy release and, consequently, Arabidopsis seed germination. This study sheds light on the intricate roles of SIF2 as a multi-functional RLK, underscoring its organ-specific contributions to plant immunity, hormonal regulation, and seed germination.

The activation of Chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its N-terminal aspartate kinase-chorismate mutase-tyrA (ACT) domain

The coordination of assimilation pathways for all the elements that make up cellular components is a vital task for every organism. Integrating the assimilation and use of carbon (C) and nitrogen (N) is of particular importance because of the high cellular abundance of these elements. Starch is one of the most important storage polymers of photosynthetic organisms, and a complex regulatory network ensures that biosynthesis and degradation of starch are coordinated with photosynthetic activity and growth. Here, we analyzed three starch metabolism enzymes of Chlamydomonas reinhardtii that we captured by a cyclic guanosine monophosphate (cGMP) affinity chromatography approach, namely, soluble starch synthase STA3, starch-branching enzyme SBE1, and α-amylase AMA2. While none of the recombinant enzymes was directly affected by the presence of cGMP or other nucleotides, suggesting an indirect binding to cGMP, AMA2 activity was stimulated in the presence of L-glutamine (Gln). This activating effect required the enzyme's N-terminal aspartate kinase-chorismate mutase-tyrA domain. Gln is the first N assimilation product and not only a central compound for the biosynthesis of N-containing molecules but also a recognized signaling molecule for the N status. Our observation suggests that AMA2 might be a means to coordinate N and C metabolism at the enzymatic level, increasing the liberation of C skeletons from starch when high Gln levels signal an abundance of assimilated N.

Pyrenoid proteomics reveals independent evolution of the CO2-concentrating organelle in chlorarachniophytes

Pyrenoids are microcompartments that are universally found in the photosynthetic plastids of various eukaryotic algae. They contain ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and play a pivotal role in facilitating CO2 assimilation via CO2-concentrating mechanisms (CCMs). Recent investigations involving model algae have revealed that pyrenoid-associated proteins participate in pyrenoid biogenesis and CCMs. However, these organisms represent only a small part of algal lineages, which limits our comprehensive understanding of the diversity and evolution of pyrenoid-based CCMs. Here we report a pyrenoid proteome of the chlorarachniophyte alga Amorphochlora amoebiformis, which possesses complex plastids acquired through secondary endosymbiosis with green algae. Proteomic analysis using mass spectrometry resulted in the identification of 154 potential pyrenoid components. Subsequent localization experiments demonstrated the specific targeting of eight proteins to pyrenoids. These included a putative Rubisco-binding linker, carbonic anhydrase, membrane transporter, and uncharacterized GTPase proteins. Notably, most of these proteins were unique to this algal lineage. We suggest a plausible scenario in which pyrenoids in chlorarachniophytes have evolved independently, as their components are not inherited from green algal pyrenoids.

Integrating cellular electron microscopy with multimodal data to explore biology across space and time

Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.

TurboID reveals the proxiomes of Chlamydomonas proteins involved in thylakoid biogenesis and stress response

In Chlamydomonas (Chlamydomonas reinhardtii), the VESICLE-INDUCING PROTEIN IN PLASTIDS 1 and 2 (VIPP1 and VIPP2) play roles in the sensing and coping with membrane stress and in thylakoid membrane biogenesis. To gain more insight into these processes, we aimed to identify proteins interacting with VIPP1/2 in the chloroplast and chose proximity labeling (PL) for this purpose. We used the transient interaction between the nucleotide exchange factor CHLOROPLAST GRPE HOMOLOG 1 (CGE1) and the stromal HEAT SHOCK PROTEIN 70B (HSP70B) as test system. While PL with APEX2 and BioID proved to be inefficient, TurboID resulted in substantial biotinylation in vivo. TurboID-mediated PL with VIPP1/2 as baits under ambient and H2O2 stress conditions confirmed known interactions of VIPP1 with VIPP2, HSP70B, and the CHLOROPLAST DNAJ HOMOLOG 2 (CDJ2). Proteins identified in the VIPP1/2 proxiomes can be grouped into proteins involved in the biogenesis of thylakoid membrane complexes and the regulation of photosynthetic electron transport, including PROTON GRADIENT REGULATION 5-LIKE 1 (PGRL1). A third group comprises 11 proteins of unknown function whose genes are upregulated under chloroplast stress conditions. We named them VIPP PROXIMITY LABELING (VPL). In reciprocal experiments, we confirmed VIPP1 in the proxiomes of VPL2 and PGRL1. Our results demonstrate the robustness of TurboID-mediated PL for studying protein interaction networks in the chloroplast of Chlamydomonas and pave the way for analyzing functions of VIPPs in thylakoid biogenesis and stress responses.

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms. Video Abstract.

The pyrenoid: the eukaryotic CO2-concentrating organelle

The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.

Chlamydomonas: Fast tracking from genomics

Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a "flagship" algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.