The role of Rubisco kinetics and pyrenoid morphology in shaping the CCM of haptophyte microalgae

Insights on the enhancement of chilling tolerance in Rice through over-expression and knock-out studies of OsRBCS3

Chilling stress is an important environmental factor that affects rice (Oryza sativa L.) growth and yield, and the booting stage is the most sensitive stage of rice to chilling stress. In this study, we focused on OsRBCS3, a rice gene related to chilling tolerance at the booting stage, which encodes the key enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit in photosynthesis. The aim of this study was to elucidate the role and mechanism of OsRBCS3 in rice chilling tolerance at the booting stage. The expression levels of OsRBCS3 under chilling stress were compared in two japonica rice cultivars with different chilling tolerances: Kongyu131 (KY131) and Longjing11 (LJ11). A positive correlation was found between OsRBCS3 expression and chilling tolerance. Over-expression (OE) and knock-out (KO) lines of OsRBCS3 were constructed using over-expression and CRISPR/Cas9 technology, respectively, and their chilling tolerance was evaluated at the seedling and booting stages. The results showed that OE lines exhibited higher chilling tolerance than wild-type (WT) lines at both seedling and booting stages, while KO lines showed lower chilling tolerance than WT lines. Furthermore, the antioxidant enzyme activities, malondialdehyde (MDA) content and Rubisco activity of four rice lines under chilling stress were measured, and it was found that OE lines had stronger antioxidant and photosynthetic capacities, while KO lines had the opposite effects. This study validated that OsRBCS3 plays an important role in rice chilling tolerance at the booting stage, providing new molecular tools and a theoretical basis for rice chilling tolerance breeding.

Multifaceted Dinoflagellates and the Marine Model Prorocentrum cordatum

BACKGROUND

Dinoflagellates are a monophyletic group within the taxon Alveolata, which comprises unicellular eukaryotes. Dinoflagellates have long been studied for their organismic and morphologic diversity as well as striking cellular features. They have a main size range of 10-100 µm, a complex "cell covering", exceptionally large genomes (∼1-250 Gbp with a mean of 50,000 protein-encoding genes) spread over a variable number of highly condensed chromosomes, and perform a closed mitosis with extranuclear spindles (dinomitosis). Photosynthetic, marine, and free-living Prorocentrum cordatum is a ubiquitously occurring, bloom-forming dinoflagellate, and an emerging model system, particularly with respect to systems biology.

SUMMARY

Focused ion beam/scanning electron microscopy (FIB/SEM) analysis of P. cordatum recently revealed (i) a flattened nucleus with unusual structural features and a total of 62 tightly packed chromosomes, (ii) a single, barrel-shaped chloroplast devoid of grana and harboring multiple starch granules, (iii) a single, highly reticular mitochondrion, and (iv) multiple phosphate and lipid storage bodies. Comprehensive proteomics of subcellular fractions suggested (i) major basic nuclear proteins to participate in chromosome condensation, (ii) composition of nuclear pores to differ from standard knowledge, (iii) photosystems I and II, chloroplast complex I, and chlorophyll a-b binding light-harvesting complex to form a large megacomplex (>1.5 MDa), and (iv) an extraordinary richness in pigment-binding proteins. Systems biology-level investigation of heat stress response demonstrated a concerted down-regulation of CO2-concentrating mechanisms, CO2-fixation, central metabolism, and monomer biosynthesis, which agrees with reduced growth yields.

KEY MESSAGES

FIB/SEM analysis revealed new insights into the remarkable subcellular architecture of P. cordatum, complemented by proteogenomic unraveling of novel nuclear structures and a photosynthetic megacomplex. These recent findings are put in the wider context of current understanding of dinoflagellates.

The diversity and coevolution of Rubisco and CO2 concentrating mechanisms in marine macrophytes

The kinetic properties of Rubisco, the most important carbon-fixing enzyme, have been assessed in a small fraction of the estimated existing biodiversity of photosynthetic organisms. Until recently, one of the most significant gaps of knowledge in Rubisco kinetics was marine macrophytes, an ecologically relevant group including brown (Ochrophyta), red (Rhodophyta) and green (Chlorophyta) macroalgae and seagrasses (Streptophyta). These organisms express various Rubisco types and predominantly possess CO2 -concentrating mechanisms (CCMs), which facilitate the use of bicarbonate for photosynthesis. Since bicarbonate is the most abundant form of dissolved inorganic carbon in seawater, CCMs allow marine macrophytes to overcome the slow gas diffusion and low CO2 availability in this environment. The present review aims to compile and integrate recent findings on the biochemical diversity of Rubisco and CCMs in the main groups of marine macrophytes. The Rubisco kinetic data provided demonstrate a more relaxed relationship among catalytic parameters than previously reported, uncovering a variability in Rubisco catalysis that has been hidden by a bias in the literature towards terrestrial vascular plants. The compiled data indicate the existence of convergent evolution between Rubisco and biophysical CCMs across the polyphyletic groups of marine macrophytes and suggest a potential role for oxygen in shaping such relationship.

Natural variation in metabolism of the Calvin-Benson cycle

The Calvin-Benson cycle (CBC) evolved over 2 billion years ago but has been subject to massive selection due to falling atmospheric carbon dioxide, rising atmospheric oxygen and changing nutrient and water availability. In addition, large groups of organisms have evolved carbon-concentrating mechanisms (CCMs) that operate upstream of the CBC. Most previous studies of CBC diversity focused on Rubisco kinetics and regulation. Quantitative metabolite profiling provides a top-down strategy to uncover inter-species diversity in CBC operation. CBC profiles were recently published for twenty species including terrestrial C3 species, terrestrial C4 species that operate a biochemical CCM, and cyanobacteria and green algae that operate different types of biophysical CCM. Distinctive profiles were found for species with different modes of photosynthesis, revealing that evolution of the various CCMs was accompanied by co-evolution of the CBC. Diversity was also found between species that share the same mode of photosynthesis, reflecting lineage-dependent diversity of the CBC. Connectivity analysis uncovers constraints due to pathway and thermodynamic topology, and reveals that cross-species diversity in the CBC is driven by changes in the balance between regulated enzymes and in the balance between the CBC and the light reactions or end-product synthesis.

Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth

Improving the carboxylation properties of Rubisco has primarily arisen from unforeseen amino acid substitutions remote from the catalytic site. The unpredictability has frustrated rational design efforts to enhance plant Rubisco towards the prized growth-enhancing carboxylation properties of red algae Griffithsia monilis GmRubisco. To address this, we determined the crystal structure of GmRubisco to 1.7 Å. Three structurally divergent domains were identified relative to the red-type bacterial Rhodobacter sphaeroides RsRubisco that, unlike GmRubisco, are expressed in Escherichia coli and plants. Kinetic comparison of 11 RsRubisco chimaeras revealed that incorporating C329A and A332V substitutions from GmRubisco Loop 6 (corresponding to plant residues 328 and 331) into RsRubisco increased the carboxylation rate (kcatc) by 60%, the carboxylation efficiency in air by 22% and the CO2/O2 specificity (Sc/o) by 7%. Plastome transformation of this RsRubisco Loop 6 mutant into tobacco enhanced photosynthesis and growth up to twofold over tobacco producing wild-type RsRubisco. Our findings demonstrate the utility of RsRubisco for the identification and in planta testing of amino acid grafts from algal Rubisco that can enhance the enzyme's carboxylase potential.

The cellular response to ocean warming in Emiliania huxleyi

Marine phytoplankton contribute substantially to the global flux of carbon from the atmosphere to the deep ocean. Sea surface temperatures will inevitably increase in line with global climate change, altering the performance of marine phytoplankton. Differing sensitivities of photosynthesis and respiration to temperature, will likely shift the strength of the future oceanic carbon sink. To further clarify the molecular mechanisms driving these alterations in phytoplankton function, shotgun proteomic analysis was carried out on the globally-occurring coccolithophore Emiliania huxleyi exposed to moderate- (23°C) and elevated- (28°C) warming. Compared to the control (17°C), growth of E. huxleyi increased under elevated temperatures, with higher rates recorded under moderate- relative to elevated- warming. Proteomic analysis revealed a significant modification of the E. huxleyi cellular proteome as temperatures increased: at lower temperature, ribosomal proteins and photosynthetic machinery appeared abundant, as rates of protein translation and photosynthetic performance are restricted by low temperatures. As temperatures increased, evidence of heat stress was observed in the photosystem, characterized by a relative down-regulation of the Photosystem II oxygen evolving complex and ATP synthase. Acclimation to elevated warming (28°C) revealed a substantial alteration to carbon metabolism. Here, E. huxleyi made use of the glyoxylate cycle and succinate metabolism to optimize carbon use, maintain growth and maximize ATP production in heat-damaged mitochondria, enabling cultures to maintain growth at levels significantly higher than those recorded in the control (17°C). Based on the metabolic changes observed, we can predict that warming may benefit photosynthetic carbon fixation by E. huxleyi in the sub-optimal to optimal thermal range. Past the thermal optima, increasing rates of respiration and costs of repair will likely constrain growth, causing a possible decline in the contribution of this species to the oceanic carbon sink depending on the evolvability of these temperature thresholds.

Eco-friendly approach for tannery effluent treatment and CO2 sequestration using unicellular green oleaginous microalga Tetradesmus obliquus TS03

The present study explored the process of bioremediation, sequestration of carbon dioxide, and biofuel production using multifarious potent freshwater microalgae Tetradesmus obliquus TS03. The heavy metals were reduced, viz., 8.34 mg of cadmium (95.13%), 4.56 mg of chromium (97.28%), 1.34 mg of copper (98.67%), 1.24 mg of cobalt (98.19%), 1.93 mg of lead (96.72%), 2.31 mg of nickel (97.14%), and 2.23 mgL^-1 of zinc (96.59%) using photobioreactor microalgal treatment method. The heavy metal biosorption capacity rate (q_max) was 98.90% determined by the Langmuir and Freundlich isotherm kinetics model at 10 days of effluent treatment using Tetradesmus obliquus TS03. The microalgae T. obliquus TS03 utilized 98.34% of carbon dioxide (CO₂) enhanced by acetyl CoA carboxylase and RuBisCO enzymes. The biodiesel was extracted from microalga and identified 32 fatty acid methyl ester major compounds viz., tetradecanoate methyl ester, hexadecanoic acid methyl ester, tridecanoic acid methyl ester, heptadecatrienoic acid methyl ester, octadecanoic acid methyl ester, eicosanoic acid methyl ester, pentadecanoic acid methyl ester, and cis-methylicosanoate using gas mass chromatography (GCMS). The biodiesel functional groups were identified, viz., amides, phenols, alcohols, alkynes, carboxylic acids, carbonyls, and ketones groups using Fourier transformation infrared (FTIR). The bioethanol was identified using high-performance liquid chromatography (HPLC) and determined the peak presented at RT of 4.35 min (75,693.1046 µV s^-1).

Carbon assimilation in upper subtidal macroalgae is determined by an inverse correlation between Rubisco carboxylation efficiency and CO2 concentrating mechanism effectiveness

Seaweeds have a wide ecophysiological and phylogenetic diversity with species expressing different Rubisco forms that frequently coexist with biophysical CO₂ concentrating mechanisms (CCMs), an adaptation that overcomes the low CO₂ availability and gas diffusion in seawater. Here, we assess the possible coevolution between the Rubisco catalysis and the type and effectiveness of CCMs present in six upper subtidal macroalgal species belonging to three phylogenetic groups of seaweeds. A wide diversity in the Rubisco kinetic traits was found across the analyzed species, although the specificity factor was the only parameter explained by the expressed Rubisco form. Differences in the catalytic trade-offs were found between Rubisco forms, indicating that ID Rubiscos could be better adapted to the intracellular O₂  : CO₂ ratio found in marine organisms during steady-state photosynthesis. The biophysical components of the CCMs also differed among macroalgal species, resulting in different effectiveness to concentrate CO₂ around Rubisco active sites. Interestingly, an inverse relationship was found between the effectiveness of CCMs and the in vitro Rubisco carboxylation efficiency, which possibly led to a similar carboxylation potential across the analyzed macroalgal species. Our results demonstrate a coevolution between Rubisco kinetics and CCMs across phylogenetically distant marine macroalgal species sharing the same environment.

The trajectory in catalytic evolution of Rubisco in Posidonia seagrass species differs from terrestrial plants

The CO2-fixing enzyme Ribulose bisphosphate carboxylase-oxygenase (Rubisco) links the inorganic and organic phases of the global carbon cycle. In aquatic systems, the catalytic adaptation of algae Rubiscos has been more expansive and followed an evolutionary pathway that appears distinct to terrestrial plant Rubisco. Here, we extend this survey to differing seagrass species of the genus Posidonia to reveal how their disjunctive geographical distribution and diverged phylogeny, along with their CO2 concentrating mechanisms (CCMs) effectiveness, have impacted their Rubisco kinetic properties. The Rubisco from Posidonia species showed lower carboxylation efficiencies and lower sensitivity to O2 inhibition than those measured for terrestrial C3 and C4-plant Rubiscos. Compared with the Australian Posidonia species, Rubisco from the Mediterranean Posidonia oceanica had 1.5-2-fold lower carboxylation and oxygenation efficiencies, coinciding with effective CCMs and five Rubisco large subunit amino acid substitutions. Among the Australian Posidonia species, CCM effectiveness was higher in Posidonia sinuosa and lower in the deep-living Posidonia angustifolia, likely related to the 20%-35% lower Rubisco carboxylation efficiency in P. sinuosa and the two-fold higher Rubisco content in P. angustifolia. Our results suggest that the catalytic evolution of Posidonia Rubisco has been impacted by the low CO2 availability and gas exchange properties of marine environments, but with contrasting Rubisco kinetics according to the time of diversification among the species. As a result, the relationships between maximum carboxylation rate and CO2- and O2-affinities of Posidonia Rubiscos follow an alternative path to that characteristic of terrestrial angiosperm Rubiscos.

Red Rubiscos and opportunities for engineering green plants

Nature's vital, but notoriously inefficient, CO2-fixing enzyme Rubisco often limits the growth of photosynthetic organisms including crop species. Form I Rubiscos comprise eight catalytic large subunits and eight auxiliary small subunits and can be classified into two distinct lineages-'red' and 'green'. While red-type Rubiscos (Form IC and ID) are found in rhodophytes, their secondary symbionts, and certain proteobacteria, green-type Rubiscos (Form IA and IB) exist in terrestrial plants, chlorophytes, cyanobacteria, and other proteobacteria. Eukaryotic red-type Rubiscos exhibit desirable kinetic properties, namely high specificity and high catalytic efficiency, with certain isoforms outperforming green-type Rubiscos. However, it is not yet possible to functionally express a high-performing red-type Rubisco in chloroplasts to boost photosynthetic carbon assimilation in green plants. Understanding the molecular and evolutionary basis for divergence between red- and green-type Rubiscos could help us to harness the superior CO2-fixing power of red-type Rubiscos. Here we review our current understanding about red-type Rubisco distribution, biogenesis, and sequence-structure, and present opportunities and challenges for utilizing red-type Rubisco kinetics towards crop improvements.

The stickers and spacers of Rubiscondensation: assembling the centrepiece of biophysical CO2-concentrating mechanisms

Aquatic autotrophs that fix carbon using ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) frequently expend metabolic energy to pump inorganic carbon towards the enzyme's active site. A central requirement of this strategy is the formation of highly concentrated Rubisco condensates (or Rubiscondensates) known as carboxysomes and pyrenoids, which have convergently evolved multiple times in prokaryotes and eukaryotes, respectively. Recent data indicate that these condensates form by the mechanism of liquid-liquid phase separation. This mechanism requires networks of weak multivalent interactions typically mediated by intrinsically disordered scaffold proteins. Here we comparatively review recent rapid developments that detail the determinants and precise interactions that underlie diverse Rubisco condensates. The burgeoning field of biomolecular condensates has few examples where liquid-liquid phase separation can be linked to clear phenotypic outcomes. When present, Rubisco condensates are essential for photosynthesis and growth, and they are thus emerging as powerful and tractable models to investigate the structure-function relationship of phase separation in biology.

Rubisco, the imperfect winner: it's all about the base

Rubisco catalysis is complex and includes an activation step through the formation of a carbamate at the conserved active site lysine residue and the formation of a highly reactive enediol that is the key to its catalytic reaction. The formation of this enediol is both the basis of its success and its Achilles' heel, creating imperfections to its catalytic efficiency. While Rubisco originally evolved in an atmosphere of high CO2, the earth's multiple oxidation events provided challenges to Rubisco through the fixation of O2 that competes with CO2 at the active site. Numerous catalytic screens across the Rubisco superfamily have identified significant variation in catalytic properties that have been linked to large and small subunit sequences. Despite this, we still have a rudimentary understanding of Rubisco's catalytic mechanism and how the evolution of kinetic properties has occurred. This review identifies the lysine base that functions both as an activator and a proton abstractor to create the enediol as a key to understanding how Rubisco may optimize its kinetic properties. The ways in which Rubisco and its partners have overcome catalytic and activation imperfections and thrived in a world of high O2, low CO2, and variable climatic regimes is remarkable.

Correlative adaptation between Rubisco and CO2-concentrating mechanisms in seagrasses

Submerged angiosperms sustain some of the most productive and diverse ecosystems worldwide. However, their carbon acquisition and assimilation mechanisms remain poorly explored, missing an important step in the evolution of photosynthesis during the colonization of aquatic environments by angiosperms. Here we reveal a convergent kinetic adaptation of Rubisco in phylogenetically distant seagrass species that share catalytic efficiencies and CO₂ and O₂ affinities up to three times lower than those observed in phylogenetically closer angiosperms from terrestrial, freshwater and brackish-water habitats. This Rubisco kinetic convergence was found to correlate with the effectiveness of seagrass CO₂-concentrating mechanisms (CCMs), which probably evolved in response to the constant CO₂ limitation in marine environments. The observed Rubisco kinetic adaptation in seagrasses more closely resembles that seen in eukaryotic algae operating CCMs rather than that reported in terrestrial C₄ plants. Our results thus demonstrate a general pattern of co-evolution between Rubisco function and biophysical CCM effectiveness that traverses distantly related aquatic lineages.

Enhanced biomass production through a repeated sequential auto-and heterotrophic culture mode in Chlorella protothecoides

A repeated sequential auto-and heterotrophic (RSAH) culture mode was designed to enhancebiomass ofChlorella protothecoides. Based on the result that the photosynthesis system may receive damage if the light period is more than 16 h, autotrophy was applied in the 16 h of the light cycle and mixotrophy using acetic acid and glucose in the 8 h of dark cycle. In the dark cycle, an organic carbon source was added according to the Monod equation to maintain activation of the TCA cycle and organic carbon source-to-cell conversion. When acetic acid and glucose were used as organic carbon sources, this culture method was found to be 32.3% and 12.6% higher in biomass, 2.59 and 2.67 times higher in the organic carbon source-to-cell conversion factor, and 2.17 and 2.32 times higher in ATP/ADP ratio, respectively, compared to mixotrophy. Through this new culture method, economic feasibility and carbon reduction capabilities in large-scale cultures can be achieved.

Targeted metabolite profiling as a top-down approach to uncover interspecies diversity and identify key conserved operational features in the Calvin-Benson cycle

Improving photosynthesis is a promising avenue to increase crop yield. This will be aided by better understanding of natural variance in photosynthesis. Profiling of Calvin-Benson cycle (CBC) metabolites provides a top-down strategy to uncover interspecies diversity in CBC operation. In a study of four C4 and five C3 species, principal components analysis separated C4 species from C3 species and also separated different C4 species. These separations were driven by metabolites that reflect known species differences in their biochemistry and pathways. Unexpectedly, there was also considerable diversity between the C3 species. Falling atmospheric CO2 and changing temperature, nitrogen, and water availability have driven evolution of C4 photosynthesis in multiple lineages. We propose that analogous selective pressures drove lineage-dependent evolution of the CBC in C3 species. Examples of species-dependent variation include differences in the balance between the CBC and the light reactions, and in the balance between regulated steps in the CBC. Metabolite profiles also reveal conserved features including inactivation of enzymes in low irradiance, and maintenance of CBC metabolites at relatively high levels in the absence of net CO2 fixation. These features may be important for photosynthetic efficiency in low light, fluctuating irradiance, and when stomata close due to low water availability.

The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae

Haptophytes are biogeochemically and industrially important protists with underexplored genomic diversity. We present a nuclear genome assembly for the class Pavlovales, which was assembled with PacBio long-read data into highly contiguous sequences. We sequenced strain Diacronema lutheri NIVA-4/92, formerly known as Pavlova lutheri, because it has established roles in aquaculture and has been a key organism for studying microalgal lipid biosynthesis. Our data show that D. lutheri has the smallest and most streamlined haptophycean genome assembled to date, with an assembly size of 43.503 Mb and 14,446 protein-coding genes. Together with its high nuclear GC content, Diacronema is an important genus for investigating selective pressures on haptophyte genome evolution, contrasting with the much larger and more repetitive genome of the coccolithophore Emiliania huxleyi. The D. lutheri genome will be a valuable resource for resolving the genetic basis of algal lipid biosynthesis and metabolic remodeling that takes place during adaptation and stress response in natural and engineered environments.

The Role of Extracellular Carbonic Anhydrase in Biogeochemical Cycling: Recent Advances and Climate Change Responses

Climate change has been predicted to influence the marine phytoplankton community and its carbon acquisition strategy. Extracellular carbonic anhydrase (eCA) is a zinc metalloenzyme that catalyses the relatively slow interconversion between HCO₃⁻ and CO₂. Early results indicated that sub-nanomolar levels of eCA at the sea surface were sufficient to enhance the oceanic uptake rate of CO₂ on a global scale by 15%, an addition of 0.37 Pg C year⁻¹. Despite its central role in the marine carbon cycle, only in recent years have new analytical techniques allowed the first quantifications of eCA and its activity in the oceans. This opens up new research areas in the field of marine biogeochemistry and climate change. Light and suitable pH conditions, as well as growth stage, are crucial factors in eCA expression. Previous studies showed that phytoplankton eCA activity and concentrations are affected by environmental stressors such as ocean acidification and UV radiation as well as changing light conditions. For this reason, eCA is suggested as a biochemical indicator in biomonitoring programmes and could be used for future response prediction studies in changing oceans. This review aims to identify the current knowledge and gaps where new research efforts should be focused to better determine the potential feedback of phytoplankton via eCA in the marine carbon cycle in changing oceans.

Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance

Diatoms are unicellular photosynthetic algae known to secrete organic matter that fuels secondary production in the ocean, though our knowledge of how their physiology impacts the composition of dissolved organic matter remains limited. Like all photosynthetic organisms, their use of light for energy and reducing power creates the challenge of avoiding cellular damage. To better understand the interplay between redox balance and organic matter secretion, we reconstructed a genome-scale metabolic model of Thalassiosira pseudonana strain CCMP 1335, a model for diatom molecular biology and physiology, with a 60-year history of studies. The model simulates the metabolic activities of 1,432 genes via a network of 2,792 metabolites produced through 6,079 reactions distributed across six subcellular compartments. Growth was simulated under different steady-state light conditions (5–200 μmol photons m^-2 s^-1) and in a batch culture progressing from exponential growth to nitrate-limitation and nitrogen-starvation. We used the model to examine the dissipation of reductants generated through light-dependent processes and found that when available, nitrate assimilation is an important means of dissipating reductants in the plastid; under nitrate-limiting conditions, sulfate assimilation plays a similar role. The use of either nitrate or sulfate uptake to balance redox reactions leads to the secretion of distinct organic nitrogen and sulfur compounds. Such compounds can be accessed by bacteria in the surface ocean. The model of the diatom Thalassiosira pseudonana provides a mechanistic explanation for the production of ecologically and climatologically relevant compounds that may serve as the basis for intricate, cross-kingdom microbial networks. Diatom metabolism has an important influence on global biogeochemistry; metabolic models of marine microorganisms link genes to ecosystems and may be key to integrating molecular data with models of ocean biogeochemistry.

Different levels of energetic coupling between photosynthesis and respiration do not determine the occurrence of adaptive responses of Symbiodiniaceae to global warming

Disentangling the metabolic functioning of corals' endosymbionts (Symbiodiniaceae) is relevant to understanding the response of coral reefs to warming oceans. In this work, we first question whether there is an energetic coupling between photosynthesis and respiration in Symbiodiniaceae (Symbiodinium, Durusdinium and Effrenium), and second, how different levels of energetic coupling will affect their adaptive responses to global warming. Coupling between photosynthesis and respiration was established by determining the variation of metabolic rates during thermal response curves, and how inhibition of respiration affects photosynthesis. Adaptive (irreversible) responses were studied by exposing two Symbiodinium species with different levels of photosynthesis-respiration interaction to high temperature conditions (32°C) for 1 yr. We found that some Symbiodiniaceae have a high level of energetic coupling; that is, photosynthesis and respiration have the same temperature dependency, and photosynthesis is negatively affected when respiration is inhibited. Conversely, photosynthesis and respiration are not coupled in other species. In any case, prolonged exposure to high temperature caused adjustments in both photosynthesis and respiration, but these changes were fully reversible. We conclude that energetic coupling between photosynthesis and respiration exhibits wide variation amongst Symbiodiniaceae and does not determine the occurrence of adaptive responses in Symbiodiniaceae to temperature increase.

The dependency of red Rubisco on its cognate activase for enhancing plant photosynthesis and growth

Plant photosynthesis and growth are often limited by the activity of the CO2-fixing enzyme Rubisco. The broad kinetic diversity of Rubisco in nature is accompanied by differences in the composition and compatibility of the ancillary proteins needed for its folding, assembly, and metabolic regulation. Variations in the protein folding needs of catalytically efficient red algae Rubisco prevent their production in plants. Here, we show this impediment does not extend to Rubisco from Rhodobacter sphaeroides (RsRubisco)-a red-type Rubisco able to assemble in plant chloroplasts. In transplastomic tobRsLS lines expressing a codon optimized Rs-rbcLS operon, the messenger RNA (mRNA) abundance was ∼25% of rbcL transcript and RsRubisco ∼40% the Rubisco content in WT tobacco. To mitigate the low activation status of RsRubisco in tobRsLS (∼23% sites active under ambient CO2), the metabolic repair protein RsRca (Rs-activase) was introduced via nuclear transformation. RsRca production in the tobRsLS::X progeny matched endogenous tobacco Rca levels (∼1 µmol protomer·m2) and enhanced RsRubisco activation to 75% under elevated CO2 (1%, vol/vol) growth. Accordingly, the rate of photosynthesis and growth in the tobRsLS::X lines were improved >twofold relative to tobRsLS. Other tobacco lines producing RsRubisco containing alternate diatom and red algae S-subunits were nonviable as CO2-fixation rates (kcatc) were reduced >95% and CO2/O2 specificity impaired 30-50%. We show differences in hybrid and WT RsRubisco biogenesis in tobacco correlated with assembly in Escherichia coli advocating use of this bacterium to preevaluate the kinetic and chloroplast compatibility of engineered RsRubisco, an isoform amenable to directed evolution.

Influence of Temperature and CO2 On Plasma-membrane Permeability to CO2 and HCO3- in the Marine Haptophytes Emiliania huxleyi and Calcidiscus leptoporus (Prymnesiophyceae)

Membrane permeabilities to CO₂ and HCO₃^- constrain the function of CO₂ concentrating mechanisms that algae use to supply inorganic carbon for photosynthesis. In diatoms and green algae, plasma membranes are moderately to highly permeable to CO₂ but effectively impermeable to HCO₃^- . Here, CO₂ and HCO₃^- membrane permeabilities were measured using an ¹⁸ O-exchange technique on two species of haptophyte algae, Emiliania huxleyi and Calcidiscus leptoporus, which showed that the plasma membranes of these species are also highly permeable to CO₂ (0.006-0.02 cm · s^-1 ) but minimally permeable to HCO₃^- . Increased temperature and CO₂ generally increased CO₂ membrane permeabilities in both species, possibly due to changes in lipid composition or CO₂ channel proteins. Changes in CO₂ membrane permeabilities showed no association with the density of calcium carbonate coccoliths surrounding the cell, which could potentially impede passage of compounds. Haptophyte plasma-membrane permeabilities to CO₂ were somewhat lower than those of diatoms but generally higher than membrane permeabilities of green algae. One caveat of these measurements is that the model used to interpret ¹⁸ O-exchange data assumes that carbonic anhydrase, which catalyzes ¹⁸ O-exchange, is homogeneously distributed in the cell. The implications of this assumption were tested using a two-compartment model with an inhomogeneous distribution of carbonic anhydrase to simulate ¹⁸ O-exchange data and then inferring plasma-membrane CO₂ permeabilities from the simulated data. This analysis showed that the inferred plasma-membrane CO₂ permeabilities are minimal estimates but should be quite accurate under most conditions.

Rubisco and carbon-concentrating mechanism co-evolution across chlorophyte and streptophyte green algae

Green algae expressing a carbon-concentrating mechanism (CCM) are usually associated with a Rubisco-containing micro-compartment, the pyrenoid. A link between the small subunit (SSU) of Rubisco and pyrenoid formation in Chlamydomonas reinhardtii has previously suggested that specific RbcS residues could explain pyrenoid occurrence in green algae. A phylogeny of RbcS was used to compare the protein sequence and CCM distribution across the green algae and positive selection in RbcS was estimated. For six streptophyte algae, Rubisco catalytic properties, affinity for CO₂ uptake (K_0.5 ), carbon isotope discrimination (δ¹³ C) and pyrenoid morphology were compared. The length of the βA-βB loop in RbcS provided a phylogenetic marker discriminating chlorophyte from streptophyte green algae. Rubisco kinetic properties in streptophyte algae have responded to the extent of inducible CCM activity, as indicated by changes in inorganic carbon uptake affinity, δ¹³ C and pyrenoid ultrastructure between high and low CO₂ conditions for growth. We conclude that the Rubisco catalytic properties found in streptophyte algae have coevolved and reflect the strength of any CCM or degree of pyrenoid leakiness, and limitations to inorganic carbon in the aquatic habitat, whereas Rubisco in extant land plants reflects more recent selective pressures associated with improved diffusive supply of the terrestrial environment.

Photosynthetic Carbon Partitioning and Metabolic Regulation in Response to Very-Low and High CO2 in Microchloropsis gaditana NIES 2587

Photosynthetic organisms fix inorganic carbon through carbon capture machinery (CCM) that regulates the assimilation and accumulation of carbon around ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). However, few constraints that govern the central carbon metabolism are regulated by the carbon capture and partitioning machinery. In order to divert the cellular metabolism toward lipids and/or biorenewables it is important to investigate and understand the molecular mechanisms of the CO2-driven carbon partitioning. In this context, strategies for enhancement of CO2 fixation which will increase the overall biomass and lipid yields, can provide clues on understanding the carbon assimilation pathway, and may lead to new targets for genetic engineering in microalgae. In the present study, we have focused on the physiological and metabolomic response occurring within marine oleaginous microalgae Microchloropsis gaditana NIES 2587, under the influence of very-low CO2 (VLC; 300 ppm, or 0.03%) and high CO2 (HC; 30,000 ppm, or 3% v/v). Our results demonstrate that HC supplementation in M. gaditana channelizes the carbon flux toward the production of long chain polyunsaturated fatty acids (LC-PUFAs) and also increases the overall biomass productivities (up to 2.0 fold). Also, the qualitative metabolomics has identified nearly 31 essential metabolites, among which there is a significant fold change observed in accumulation of sugars and alcohols such as galactose and phytol in VLC as compared to HC. In conclusion, our focus is to understand the entire carbon partitioning and metabolic regulation within these photosynthetic cell factories, which will be further evaluated through multiomics approach for enhanced productivities of biomass, biofuels, and bioproducts (B3).

Insights on the Functions and Ecophysiological Relevance of the Diverse Carbonic Anhydrases in Microalgae

Carbonic anhydrases (CAs) exist in all kingdoms of life. They are metalloenzymes, often containing zinc, that catalyze the interconversion of bicarbonate and carbon dioxide-a ubiquitous reaction involved in a variety of cellular processes. So far, eight classes of apparently evolutionary unrelated CAs that are present in a large diversity of living organisms have been described. In this review, we focus on the diversity of CAs and their roles in photosynthetic microalgae. We describe their essential role in carbon dioxide-concentrating mechanisms and photosynthesis, their regulation, as well as their less studied roles in non-photosynthetic processes. We also discuss the presence in some microalgae, especially diatoms, of cambialistic CAs (i.e., CAs that can replace Zn by Co, Cd, or Fe) and, more recently, a CA that uses Mn as a metal cofactor, with potential ecological relevance in aquatic environments where trace metal concentrations are low. There has been a recent explosion of knowledge about this well-known enzyme with exciting future opportunities to answer outstanding questions using a range of different approaches.

Photons to food: genetic improvement of cereal crop photosynthesis

Photosynthesis has become a major trait of interest for cereal yield improvement as breeders appear to have reached the theoretical genetic limit for harvest index, the mass of grain as a proportion of crop biomass. Yield improvements afforded by the adoption of green revolution dwarfing genes to wheat and rice are becoming exhausted, and improvements in biomass and radiation use efficiency are now sought in these crops. Exploring genetic diversity in photosynthesis is now possible using high-throughput techniques, and low-cost genotyping facilitates discovery of the genetic architecture underlying this variation. Photosynthetic traits have been shown to be highly heritable, and significant variation is present for these traits in available germplasm. This offers hope that breeding for improved photosynthesis and radiation use efficiency in cereal crops is tractable and a useful shorter term adjunct to genetic and genome engineering to boost yield potential.

Conversion of NaHCO3 to Na2 CO3 with a growth of Arthrospira platensis cells in 660 m2 raceway ponds with a CO2 bicarbonation absorber

The weight ratio of Na2 CO3 /NaHCO3 was investigated in order to improve microalgal productivity in large-scale industrial operations by converting NaHCO3 to Na2 CO3 with a growth of Arthrospira platensis cells in 660 m2 raceway ponds. Two microalgal cultivation systems with a NaHCO3 by-product (SPBP) and a CO2 bicarbonation absorber (CBAP) were firstly thoroughly introduced. There was a 13.3% decrease in the initial weight ratio of Na2 CO3 /NaHCO3 resulting in a 25.3% increase in the biomass growth rate with CBAP, compared to that of SPBP. Increased sunlight intensity, solution temperature and pH all resulted in both a higher HCO 3 - absorbance and CO 3 2 - release, thereby increasing the weight ratio of Na2 CO3 /NaHCO3 during the growth of A. platensis. The biomass growth rate was peaked at 39.9 g m-2  day-1 when the weight ratio of Na2 CO3 /NaHCO3 was 3.7. Correspondingly, the cell pigments (chlorophyll a and carotenoid) and trichome size (helix pitch and trichome length) reached to a maximum state of 8.47 mg l-1 , 762 μg l-1 , 57 and 613 μm under the CBAP system.

Evolutionary trends in RuBisCO kinetics and their co-evolution with CO2 concentrating mechanisms

RuBisCO-catalyzed CO₂ fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5-bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen-rich atmosphere promoted the appearance of CO₂ concentrating mechanisms (CCMs) and/or the evolution of a more CO₂ -specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO₂ /O₂ concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co-evolution of RuBisCO and CCMs. Trade-offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO₂ specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.

Photorespiration in the context of Rubisco biochemistry, CO2 diffusion and metabolism

Photorespiratory metabolism is essential for plants to maintain functional photosynthesis in an oxygen-containing environment. Because the oxygenation reaction of Rubisco is followed by the loss of previously fixed carbon, photorespiration is often considered a wasteful process and considerable efforts are aimed at minimizing the negative impact of photorespiration on the plant's carbon uptake. However, the photorespiratory pathway has also many positive aspects, as it is well integrated within other metabolic processes, such as nitrogen assimilation and C₁ metabolism, and it is important for maintaining the redox balance of the plant. The overall effect of photorespiratory carbon loss on the net CO₂ fixation of the plant is also strongly influenced by the physiology of the leaf related to CO₂ diffusion. This review outlines the distinction between Rubisco oxygenation and photorespiratory CO₂ release as a basis to evaluate the costs and benefits of photorespiration.

Upper ocean oxygenation, evolution of RuBisCO and the Phanerozoic succession of phytoplankton

Evidence is compiled to demonstrate a redox scale within Earth's photosynthesisers that correlates the specificity of their RuBisCO with organismal metabolic tolerance to anoxia, and ecological selection by dissolved O2/CO2 and nutrients. The Form 1B RuBisCO found in the chlorophyte green algae, has a poor selectivity between the two dissolved substrates, O2 and CO2, at the active site. This enzyme appears adapted to lower O2/CO2 ratios, or more "anoxic" conditions and therefore requires additional energetic or nutrient investment in a carbon concentrating mechanism (CCM) to boost the intracellular CO2/O2 ratio and maintain competitive carboxylation rates under increasingly high O2/CO2 conditions in the environment. By contrast the coccolithophores and diatoms evolved containing the more selective Rhodophyte Form 1D RuBisCO, better adapted to a higher O2/CO2 ratio, or more oxic conditions. This Form 1D RuBisCO requires lesser energetic or nutrient investment in a CCM to attain high carboxylation rates under environmentally high O2/CO2 ratios. Such a physiological relationship may underpin the succession of phytoplankton in the Phanerozoic oceans: the coccolithophores and diatoms took over the oceanic realm from the incumbent cyanobacteria and green algae when the upper ocean became persistently oxygenated, alkaline and more oligotrophic. The facultatively anaerobic green algae, able to tolerate the anoxic conditions of the water column and a periodically inundated soil, were better poised to adapt to the fluctuating anoxia associated with periods of submergence and emergence and transition onto the land. The induction of a CCM may exert a natural limit to the improvement of RuBisCO efficiency over Earth history. Rubisco specificity appears to adapt on the timescale of ∼100 Myrs. So persistent elevation of CO2/O2 ratios in the intracellular environment around the enzyme, may induce a relaxation in RuBisCO selectivity for CO2 relative to O2. The most efficient RuBisCO for net carboxylation is likely to be found in CCM-lacking algae that have been exposed to hyperoxic conditions for at least 100 Myrs, such as intertidal brown seaweeds.

Potential improvement of photosynthetic CO2 assimilation in crops by exploiting the natural variation in the temperature response of Rubisco catalytic traits

The enhancement of the photosynthetic capacity of crops by the expression of more efficient Rubisco versions has been a main target in the field of plant photosynthesis improvement. However, such an increase in the photosynthetic efficiency will depend on the environmental conditions and on the responsiveness of Rubisco to temperature and CO₂ availability. After an exhaustive compilation and standardization of the data published so far, a large natural variability in the thermal responses of Rubisco kinetic parameters in higher plant species was revealed. The variability observed was related to the photosynthetic type but a limited adaptation to the species thermal environment was found. We provide theoretical evidence that the existence of distinctive Rubisco responses to varying temperature and CO₂ concentration constitutes a promising avenue for increasing the photosynthetic capacity of important crops under future climatic conditions.

Rubisco carboxylation kinetics and inorganic carbon utilization in polar versus cold-temperate seaweeds

Despite the high productivity and ecological importance of seaweeds in polar coastal regions, little is known about their carbon utilization mechanisms, especially the kinetics of the CO2-fixing enzyme Rubisco. We analyzed Rubisco carboxylation kinetics at 4 °C and 25 °C in 12 diverse polar seaweed species (including cold-temperate populations of the same species) and the relationship with their ability to use bicarbonate, by using 13C isotope discrimination and pH drift experiments. We observed a large variation in Rubisco carboxylation kinetics among the selected species, although no correlation was found between either the Michaelis-Menten constant for CO2 (Kc) or Rubisco content per total soluble protein ([Rubisco]/[TSP]) and the ability to use bicarbonate for non-green seaweeds. This study reports intraspecific Rubisco cold adaptation by means of either higher Rubisco carboxylation turnover rate (kcatc) and carboxylase efficiency (kcatc/Kc) at 4 °C or higher [Rubisco]/[TSP] in some of the analyzed species. Our data point to a widespread ability for photosynthetic bicarbonate usage among polar seaweeds, despite the higher affinity of Rubisco for CO2 and higher dissolved CO2 concentration in cold seawater. Moreover, the reported catalytic variation within form ID Rubisco might avert the canonical trade-off previously observed between Kc and kcatc for plant Rubiscos.

The global mass and average rate of rubisco

Rubisco is often claimed to be the most abundant protein on Earth, yet the quantitative evidence to support the estimate of its global mass are scarce. Here we provide a robust and detailed estimate of the global mass of Rubisco, which is an order of magnitude larger than previous estimates. We use this estimate to derive the time-average rate of terrestrial and marine Rubisco and show that they are, respectively, 100-fold and sevenfold lower than the in vitro measured k_cat of Rubisco at 25 °C.

Photosynthetic carbon assimilation enables energy storage in the living world and produces most of the biomass in the biosphere. Rubisco (d-ribulose 1,5-bisphosphate carboxylase/oxygenase) is responsible for the vast majority of global carbon fixation and has been claimed to be the most abundant protein on Earth. Here we provide an updated and rigorous estimate for the total mass of Rubisco on Earth, concluding it is ≈0.7 Gt, more than an order of magnitude higher than previously thought. We find that >90% of Rubisco enzymes are found in the ≈2 × 10¹⁴ m² of leaves of terrestrial plants, and that Rubisco accounts for ≈3% of the total mass of leaves, which we estimate at ≈30 Gt dry weight. We use our estimate for the total mass of Rubisco to derive the effective time-averaged catalytic rate of Rubisco of ≈0.03 s⁻¹ on land and ≈0.6 s⁻¹ in the ocean. Compared with the maximal catalytic rate observed in vitro at 25 °C, the effective rate in the wild is ≈100-fold slower on land and sevenfold slower in the ocean. The lower ambient temperature, and Rubisco not working at night, can explain most of the difference from laboratory conditions in the ocean but not on land, where quantification of many more factors on a global scale is needed. Our analysis helps sharpen the dramatic difference between laboratory and wild environments and between the terrestrial and marine environments.

Closing the circle

In Chlamydomonas the different stages of the Calvin-Benson cycle take place in separate locations within the chloroplast.

Engineering photosynthesis: progress and perspectives

Photosynthesis is the basis of primary productivity on the planet. Crop breeding has sustained steady improvements in yield to keep pace with population growth increases. Yet these advances have not resulted from improving the photosynthetic process per se but rather of altering the way carbon is partitioned within the plant. Mounting evidence suggests that the rate at which crop yields can be boosted by traditional plant breeding approaches is wavering, and they may reach a “yield ceiling” in the foreseeable future. Further increases in yield will likely depend on the targeted manipulation of plant metabolism. Improving photosynthesis poses one such route, with simulations indicating it could have a significant transformative influence on enhancing crop productivity. Here, we summarize recent advances of alternative approaches for the manipulation and enhancement of photosynthesis and their possible application for crop improvement.