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

Diverse inorganic carbon uptake strategies in Antarctic seaweeds: Revealing species-specific responses and implications for Ocean Acidification

Seaweeds are important components of coastal benthic ecosystems along the Western Antarctic Peninsula (WAP), providing refuge, food, and habitat for numerous associated species. Despite their crucial role, the WAP is among the regions most affected by global climate change, potentially impacting the ecology and physiology of seaweeds. Elevated atmospheric CO2 concentrations have led to increased dissolved inorganic carbon (Ci) with consequent declines in oceanic pH and alterations in seawater carbonate chemistry, known as Ocean Acidification (OA). Seaweeds possess diverse strategies for Ci uptake, including CO2 concentrating mechanisms (CCMs), which may distinctly respond to changes in Ci concentrations. Conversely, some seaweeds do not operate CCMs (non-CCM species) and rely solely on CO2. Nevertheless, our understanding of the status and functionality of Ci uptake strategies in Antarctic seaweeds remains limited. Here, we investigated the Ci uptake strategies of seaweeds along a depth gradient in the WAP. Carbon isotope signatures (δ13C) and pH drift assays were used as indicators of the presence or absence of CCMs. Our results reveal variability in CCM occurrence among algal phyla and depths ranging from 0 to 20 m. However, this response was species specific. Among red seaweeds, the majority relied solely on CO2 as an exogenous Ci source, with a high percentage of non-CCM species. Green seaweeds exhibited depth-dependent variations in CCM status, with the proportion of non-CCM species increasing at greater depths. Conversely, brown seaweeds exhibited a higher prevalence of CCM species, even in deep waters, indicating the use of CO2 and HCO3-. Our results are similar to those observed in temperate and tropical regions, indicating that the potential impacts of OA on Antarctic seaweeds will be species specific. Additionally, OA may potentially increase the abundance of non-CCM species relative to those with CCMs.

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.

Chloroplast-targeted late embryogenesis abundant 1 increases alfalfa tolerance to drought and aluminum

Late embryogenesis-abundant (LEA) proteins are important stress-response proteins that participate in protecting plants against abiotic stresses. Here, we investigated LEA group 3 protein MsLEA1, containing the typically disordered and α-helix structure, via overexpression and RNA interference (RNAi) approaches in alfalfa (Medicago sativa L.) under drought and aluminum (Al) stresses. MsLEA1 was highly expressed in leaves and localized in chloroplasts. Overexpressing MsLEA1 increased alfalfa tolerance to drought and Al stresses, but downregulating MsLEA1 decreased the tolerance. We observed a larger stomatal aperture and a lower water use efficiency in MsLEA1 RNAi lines compared with wild-type plants under drought stress. Photosynthetic rate, Rubisco activity, and superoxide dismutase (SOD) activity increased or decreased in MsLEA1-OE or MsLEA1-RNAi lines, respectively, under drought and Al stress. Copper/zinc SOD (Cu/Zn-SOD), iron SOD (Fe-SOD), and Rubisco large subunit proteins (Ms1770) were identified as binding partners of MsLEA1, which protected chloroplast structure and function under drought and Al stress. These results indicate that MsLEA1 recruits and protects its target proteins (SOD and Ms1770) and increases alfalfa tolerance against drought and Al stresses.

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.

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.

Anatomical and biochemical evolutionary ancient traits of Araucaria araucana (Molina) K. Koch and their effects on carbon assimilation

The study of ancient species provides valuable information concerning the evolution of specific adaptations to past and current environmental conditions. Araucaria araucana (Molina) K. Koch belongs to one of the oldest families of conifers in the world, but despite this, there are few studies focused on its physiology and responses to changes in environmental conditions. We used an integrated approach aimed at comprehensively characterizing the ecophysiology of this poorly known species, focusing in its stomatal, mesophyll and biochemical traits, hypothesizing that these traits govern the carbon assimilation of A. araucana under past and present levels of atmospheric CO2. Results indicated that A. araucana presents the typical traits of an ancient species, such as large stomata and low stomatal density, which trigger low stomatal conductance and slow stomatal responsiveness to changing environmental conditions. Interestingly, the quantitative analysis showed that photosynthetic rates were equally limited by both diffusive and biochemical components. The Rubisco catalytic properties proved to have a low Rubisco affinity for CO2 and O2, similar to other ancient species. This affinity for CO2, together with the low carboxylation turnover rate, are responsible for the low Rubisco catalytic efficiency of carboxylation. These traits could be the result of the diverse environmental selective pressures that A. araucana was exposed during its diversification. The increase in measured temperatures induced an increase in stomatal and biochemical limitations, which together with a lower Rubisco affinity for CO2 could explain the low photosynthetic capacity of A. araucana in warmer conditions.

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.

High-CO2 Levels Rather than Acidification Restrict Emiliania huxleyi Growth and Performance

The coccolithophore Emiliania huxleyi shows a variety of responses to ocean acidification (OA) and to high-CO₂ concentrations, but there is still controversy on differentiating between these two factors when using different strains and culture methods. A heavily calcified type A strain isolated from the Norwegian Sea was selected and batch cultured in order to understand whether acclimation to OA was mediated mainly by CO₂ or H⁺, and how it impacted cell growth performance, calcification, and physiological stress management. Emiliania huxleyi responded differently to each acidification method. CO₂-enriched aeration (1200 µatm, pH 7.62) induced a negative effect on the cells when compared to acidification caused by decreasing pH alone (pH 7.60). The growth rates of the coccolithophore were more negatively affected by high pCO₂ than by low pH without CO₂ enrichment with respect to the control (400 µatm, pH 8.1). High CO₂ also affected cell viability and promoted the accumulation of reactive oxygen species (ROS), which was not observed under low pH. This suggests a possible metabolic imbalance induced by high CO₂ alone. In contrast, the affinity for carbon uptake was negatively affected by both low pH and high CO₂. Photochemistry was only marginally affected by either acidification method when analysed by PAM fluorometry. The POC and PIC cellular quotas and the PIC:POC ratio shifted along the different phases of the cultures; consequently, calcification did not follow the same pattern observed in cell stress and growth performance. Specifically, acidification by HCl addition caused a higher proportion of severely deformed coccoliths, than CO₂ enrichment. These results highlight the capacity of CO₂ rather than acidification itself to generate metabolic stress, not reducing calcification.

Analyzing the causes of method-to-method variability among Rubisco kinetic traits: from the first to the current measurements

Due to the importance of Rubisco in the biosphere, its kinetic parameters have been measured by different methodologies in a large number of studies over the last 60 years. These parameters are essential to characterize the natural diversity in the catalytic properties of the enzyme and they are also required for photosynthesis and cross-scale crop modeling. The present compilation of Rubisco kinetic parameters in model species revealed a wide intraspecific laboratory-to-laboratory variability, which was partially solved by making corrections to account for differences in the assay buffer composition and in the acidity constant of dissolved CO2, as well as for differences in the CO2 and O2 solubilities. Part of the intraspecific variability was also related to the different analytical methodologies used. For instance, significant differences were found between the two main methods for the determination of the specificity factor (Sc/o), and also between Rubisco quantification methods, Rubisco purification versus crude extracts, and single-point versus CO2 curve measurements for the carboxylation turnover rate (kcatc) determination. Causes of the intraspecific laboratory-to-laboratory variability for Rubisco catalytic traits are discussed. This study provides a normalized kinetic dataset for model species to be used by the scientific community. Corrections and recommendations are also provided to reduce measurement variability, allowing the comparison of kinetic data obtained in different laboratories using different assay conditions.

Photosynthetic Characteristics of Three Cohabitated Macroalgae in the Daya Bay, and Their Responses to Temperature Rises

Biochemical compositions and photosynthetic characteristics of three naturally cohabitated macroalgae, Ulva fasciata, Sargassum hemiphyllum and Grateloupia livida, were comparably explored in the field conditions in Daya Bay, northern South China Sea, as well as their responses to temperature rise. Chlorophyll a (Chl a) and carotenoids contents of U. fasciata were 1.00 ± 0.15 and 0.57 ± 0.08 mg g^-1 in fresh weight (FW), being about one- and two-fold higher than that of S. hemiphyllum and G. livida; and the carbohydrate content was 20.3 ± 0.07 mg g^-1 FW, being about three- and one-fold higher, respectively. Throughout the day, the maximal photochemical quantum yield (F_V/F_M) of Photosystem II (PS II) of these three macroalgae species decreased from morning to noon, then increased to dusk and kept steady at nighttime. Consistently, the rapid light curve-derived light utilization efficiency (α) and maximum relative electron transfer rate (rETRmax) were lower at noon than that at morning- or night-time. The F_V/F_M of U. fasciata (varying from 0.78 to 0.32) was 38% higher than that of G. livida throughout the day, and that of S. hemiphyllum was intermediate. The superoxide dismutase (SOD) and catalase (CAT) activities in U. fasciata were lower than that in S. hemiphyllum and G. livida. Moreover, the rises in temperature species-specifically mediated the damage (k) caused by stressful high light and the corresponding repair (r) to photosynthetic apparatus, making the r/k ratio increase with the rising temperature in U. fasciata, unchanged in S. hemiphyllum but decreased in G. livida. Our results indicate that U. fasciata may compete with S. hemiphyllum or G. livida and dominate the macroalgae community under aggravatedly warming future in the Daya Bay.

Rubisco substitutions predicted to enhance crop performance through carbon uptake modelling

Improving the performance of the CO2-fixing enzyme Rubisco is among the targets for increasing crop yields. Here, Earth system model (ESM) representations of canopy C3 and C4 photosynthesis were combined with species-specific Rubisco parameters to quantify the consequences of bioengineering foreign Rubiscos into C3 and C4 crops under field conditions. The 'two big leaf' (sunlit/shaded) model for canopy photosynthesis was used together with species-specific Rubisco kinetic parameters including maximum rate (Kcat), Michaelis-Menten constant for CO2 at ambient atmospheric O2 (Kc21%O2), specificity for CO2 to O2 (Sc/o), and associated heat activation (Ha) values. Canopy-scale consequences of replacing native Rubiscos in wheat, maize, and sugar beet with foreign enzymes from 27 species were modelled using data from Ameriflux and Fluxnet databases. Variation among the included Rubisco kinetics differentially affected modelled carbon uptake rates, and Rubiscos from several species of C4 grasses showed the greatest potential of >50% carbon uptake improvement in wheat, and >25% improvement in sugar beet and maize. This study also reaffirms the need for data on fully characterized Rubiscos from more species, and for better parameterization of 'Vcmax' and temperature response of 'Jmax' in ESMs.

Inorganic carbon uptake strategies in coralline algae: Plasticity across evolutionary lineages under ocean acidification and warming

Dissolved inorganic carbon (DIC) assimilation is essential to the reef-building capacity of crustose coralline algae (CCA). Little is known, however, about the DIC uptake strategies and their potential plasticity under ongoing ocean acidification (OA) and warming. The persistence of CCA lineages throughout historical oscillations of pCO₂ and temperature suggests that evolutionary history may play a role in selecting for adaptive traits. We evaluated the effects of pCO₂ and temperature on the plasticity of DIC uptake strategies and associated energetic consequences in reef-building CCA from different evolutionary lineages. We simulated past, present, moderate (IPCC RCP 6.0) and high pCO₂ (RCP 8.5) and present and high (RCP 8.5) temperature conditions and quantified stable carbon isotope fractionation (¹³ε), organic carbon content, growth and photochemical efficiency. All investigated CCA species possess CO₂-concentrating mechanisms (CCMs) and assimilate CO₂ via diffusion to varying degrees. Under OA and warming, CCA either increased or maintained CCM capacity, which was associated with overall neutral effects on metabolic performance. More basal taxa, Sporolithales and Hapalidiales, had greater capacity for diffusive CO₂ use than Corallinales. We suggest that CCMs are an adaptation that supports a robust carbon physiology and are likely responsible for the endurance of CCA in historically changing oceans.

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.