The mechanism of Rubisco‐catalysed oxygenation

Ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) is the cornerstone of photosynthetic carbon assimilation because it catalyses the fixation of CO₂ onto ribulose‐1,5‐bisphosphate (RuBP). The enzyme also catalyses RuBP oxygenation, thereby evolving phosphoglycolate which is recycled along the photorespiratory pathway. Oxygenation is quantitatively important, because under ordinary gaseous conditions, more than one third of RuBP molecules are oxygenated rather than carboxylated. However, contrary to carboxylation, the chemical mechanism of oxygenation is not well known, and little progress has been made since the early 80s. Here, I review recent experimental data that provide some new insights into the reaction mechanism, and carry out simple calculations of kinetic parameters. Isotope effects suggest that oxygenation is less likely initiated by a redox phenomenon (such as superoxide production) and more likely involves concerted chemical events that imply interactions with protons. A possible energy profile of the reaction is drawn which suggests that the generation of the oxygenated reaction intermediate (peroxide) is irreversible. Possible changes in oxygenation‐associated rate constants between Rubisco forms are discussed.     

Estimation of rate constants of the partial reactions of carboxylation of ribulose-1,5-bisphosphate in vivo

An in vivo method for the estimation of kinetic parameters of partial reactions of carboxylation of ribulose 1,5-bisphosphate (RuBP) catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is described. Rubisco in barley, wheat and bean is different in the ability of its active centers to bind RuBP. The rate constant of the formation of the Rubisco-RuBP complex in these plants at 25 °C is 0.414, 0.245 and 0.660 mM^-1 s^-1, respectively. The rate constant of the reaction of the Rubisco-bound enediol with CO₂ does not differ significantly in barley and wheat, and averages 66 mM^-1 s^-1. Decreased irradiance inhibits Rubisco in two ways: by reducing the concentration of operating catalytic sites and by decreasing the rate constant of binding of RuBP to Rubisco. High concentrations of CO₂ inhibit Rubisco by decreasing the concentration of competent carboxylation centers, without any s ignificant influence upon the rate constants of partial reactions.     

Characterization of Chlamydomonas Ribulose-1,5-bisphosphate carboxylase/oxygenase variants mutated at residues that are post-translationally modified

BackgroundRibulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the chloroplast enzyme that fixes CO₂ in photosynthesis, but the enzyme also fixes O₂, which leads to the wasteful photorespiratory pathway. If we better understand the structure-function relationship of the enzyme, we might be able to engineer improvements. When the crystal structure of Chlamydomonas Rubisco was solved, four new posttranslational modifications were observed which are not present in other species. The modifications were 4-hydroxylation of the conserved Pro-104 and 151 residues, and S-methylation of the variable Cys-256 and 369 residues, which are Phe-256 and Val-369 in land plants. Because the modifications were only observed in Chlamydomonas Rubisco, they might account for the differences in kinetic properties between the algal and plant enzymes.MethodsSite-directed mutagenesis and chloroplast transformation have been used to test the essentiality of these modifications by replacing each of the residues with alanine (Ala). Biochemical analyses were done to determine the specificity factors and kinetic constants.ResultsReplacing the modified-residues in Chlamydomonas Rubisco affected the enzyme's catalytic activity. Substituting hydroxy-Pro-104 and methyl-Cys-256 with alanine influenced Rubisco catalysis.ConclusionThis is the first study on these posttranslationally-modified residues in Rubisco by genetic engineering. As these forms of modifications/regulation are not available in plants, the modified residues could be a means to modulate Rubisco activity.General significanceWith a better understanding of Rubisco structure-function, we can define targets for improving the enzyme.     

Transgenic tobacco plants with improved cyanobacterial Rubisco expression but no extra assembly factors grow at near wild‐type rates if provided with elevated CO2

Introducing a carbon‐concentrating mechanism and a faster Rubisco enzyme from cyanobacteria into higher plant chloroplasts may improve photosynthetic performance by increasing the rate of CO₂ fixation while decreasing losses caused by photorespiration. We previously demonstrated that tobacco plants grow photoautotrophically using Rubisco from Synechococcus elongatus, although the plants exhibited considerably slower growth than wild‐type and required supplementary CO₂. Because of concerns that vascular plant assembly factors may not be adequate for assembly of a cyanobacterial Rubisco, prior transgenic plants included the cyanobacterial chaperone RbcX or the carboxysomal protein CcmM35. Here we show that neither RbcX nor CcmM35 is needed for assembly of active cyanobacterial Rubisco. Furthermore, by altering the gene regulatory sequences on the Rubisco transgenes, cyanobacterial Rubisco expression was enhanced and the transgenic plants grew at near wild‐type growth rates, although still requiring elevated CO₂. We performed detailed kinetic characterization of the enzymes produced with and without the RbcX and CcmM35 cyanobacterial proteins. These transgenic plants exhibit photosynthetic characteristics that confirm the predicted benefits of introduction of non‐native forms of Rubisco with higher carboxylation rate constants in vascular plants and the potential nitrogen‐use efficiency that may be achieved provided that adequate CO₂ is available near the enzyme.     

Simple Determination of the CO(2)/O(2) Specificity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase by the Specific Radioactivity of [C]Glycerate 3-Phosphate

A new method is presented for measurement of the CO₂/O₂ specificity factor of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The [¹⁴C]3-phosphoglycerate (PGA) from the Rubisco carboxylase reaction and its dilution by the Rubisco oxygenase reaction was monitored by directly measuring the specific radioactivity of PGA. ¹⁴CO₂ fixation with Rubisco occurred under two reaction conditions: carboxylase with oxygenase with 40 micromolar CO₂ in O₂-saturated water and carboxylase only with 160 micromolar CO₂ under N₂. Detection of the specific radioactivity used the amount of PGA as obtained from the peak area, which was determined by pulsed amperometry following separation by high-performance anion exchange chromatography and the radioactive counts of the [¹⁴C]PGA in the same peak. The specificity factor of Rubisco from spinach (Spinacia oleracea L.) (93 ± 4), from the green alga Chlamydomonas reinhardtii (66 ± 1), and from the photosynthetic bacterium Rhodospirillum rubrum (13) were comparable with the published values measured by different methods.     

Responses of carboxylating enzymes,sucrose metabolizing enzymes and plant hormones in a tropical epiphytic CAM orchid to CO2 enrichment

After exposure to a doubled CO₂ concentration of 750 µL L^?1 for 2 months, average relative growth rate (RGR) of Mokara Yellow increased 25%. The two carboxylating enzymes, ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) and phosphoenolpyruvate carboxylase (PEPCase), responded differently to CO₂ enrichment. There was a significant daytime down‐regulation in Rubisco activity in the leaves of CO₂‐enriched plants. However, PEPCase activity in CO₂‐enriched plants was much higher in the dark period, although it was slightly lower during the daytime than that at ambient CO₂. Leaf sucrose–phosphate synthase (SPS) and sucrose synthase (SS) activities in CO₂‐enriched plants increased markedly, along with a night‐time increase in total titratable acidity and malate accumulation. There was a remarkable increase in the levels of indole‐3‐acetic acid (IAA), gibberellins A₁ and A₃ (GA₁₊₃), isopentenyladenosine (iPA) and zeatin riboside (ZR) in the expanding leaves of plants grown at elevated CO₂. It is suggested that (1) the down‐regulation of Rubisco and up‐regulation of SPS and SS are two important acclimation processes that are beneficial because it enhanced both photosynthetic capacity at high CO₂ and reduced resource investment in excessive Rubisco capacity; (2) the increased levels of plant hormones in CO₂‐enriched M. Yellow might play an important role in controlling its growth and development.     

Temperature response of in vivo Rubisco kinetics and mesophyll conductance in Arabidopsis thaliana: comparisons to Nicotiana tabacum

Biochemical models are used to predict and understand the response of photosynthesis to rising temperatures and CO₂ partial pressures. These models require the temperature dependency of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) kinetics and mesophyll conductance to CO₂ (g_m). However, it is not known how the temperature response of Rubisco kinetics differs between species, and comprehensive in vivo Rubisco kinetics that include g_m have only been determined in the warm‐adapted Nicotiana tabacum. Here, we measured the temperature response of Rubisco kinetics and g_m in N. tabacum and the cold‐adapted Arabidopsis thaliana using gas exchange and ¹³CO₂ isotopic discrimination on plants with genetically reduced levels of Rubisco. While the individual Rubisco kinetic parameters in N. tabacum and A. thaliana were similar across temperatures, they collectively resulted in significantly different modelled rates of photosynthesis. Additionally, g_m increased with temperature in N. tabacum but not in A. thaliana. These findings highlight the importance of considering species‐dependent differences in Rubisco kinetics and g_m when modelling the temperature response of photosynthesis.     

Expanding knowledge of the Rubisco kinetics variability in plant species: environmental and evolutionary trends

The present study characterizes the kinetic properties of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) from 28 terrestrial plant species, representing different phylogenetic lineages, environmental adaptations and photosynthetic mechanisms. Our findings confirm that past atmospheric CO₂/O₂ ratio changes and present environmental pressures have influenced Rubisco kinetics. One evolutionary adaptation to a decreasing atmospheric CO₂/O₂ ratio has been an increase in the affinity of Rubisco for CO₂ (K_c falling), and a consequent decrease in the velocity of carboxylation (k_cat^c), which in turn has been ameliorated by an increase in the proportion of leaf protein accounted by Rubisco. The trade‐off between K_c and k_cat^c was not universal among the species studied and deviations from this relationship occur in extant forms of Rubisco. In species adapted to particular environments, including carnivorous plants, crassulacean acid metabolism species and C₃ plants from aquatic and arid habitats, Rubisco has evolved towards increased efficiency, as demonstrated by a higher k_cat^c/K_c ratio. This variability in kinetics was related to the amino acid sequence of the Rubisco large subunit. Phylogenetic analysis identified 13 residues under positive selection during evolution towards specific Rubisco kinetic parameters. This crucial information provides candidate amino acid replacements, which could be implemented to optimize crop photosynthesis under a range of environmental conditions.     

Fallover of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase Activity : Decarbamylation of Catalytic Sites Depends on pH

Loss of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) activity during CO₂ fixation, called fallover, occurred with or without loss of activator CO₂ from catalytic sites depending on pH. At pH 7.5, but not at pH 8.5, the fraction of Rubisco sites that were carbamylated decreased during fallover. Inhibitors which formed during fallover were identified following NaBH₄ reduction and separation of the products by high performance anion-exchange chromatography and pulsed amperometric detection. They were xylulose 1,5-bisphosphate (XuBP) and 3-ketoarabinitol 1,5-bisphosphate. During fallover at pH 8.5, 3-ketoarabinitol-P₂ was the only inhibitor binding to Rubisco and this binding was at carbamylated sites, although both inhibitors were made. At pH 7.5, both inhibitors were bound to catalytic sites of Rubisco with XuBP bound tightly to decarbamylated sites, whereas 3-ketoarabinitol-P₂ bound to carbamylated sites. The pH during fallover also influenced the ratio of 3-ketoarabinitol-P₂ to XuBP formed. When fallover occurred at pH 7.5, both the formation of XuBP and its binding affinity to decarbamylated Rubisco sites were increased compared with those at pH 8.5. 3-Ketoribitol-P₂ was not found at either pH.     

Photorespiration and carbon concentrating mechanisms: two adaptations to high O2, low CO2 conditions

This review presents an overview of the two ways that cyanobacteria, algae, and plants have adapted to high O₂ and low CO₂ concentrations in the environment. First, the process of photorespiration enables photosynthetic organisms to recycle phosphoglycolate formed by the oxygenase reaction catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Second, there are a number of carbon concentrating mechanisms that increase the CO₂ concentration around Rubisco which increases the carboxylase reaction enhancing CO₂ fixation. This review also presents possibilities for the beneficial modification of these processes with the goal of improving future crop yields.     

Functional Hybrid Rubisco Enzymes with Plant Small Subunits and Algal Large Subunits: ENGINEERED rbcS cDNA FOR EXPRESSION IN CHLAMYDOMONAS*?

There has been much interest in the chloroplast-encoded large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) as a target for engineering an increase in net CO₂ fixation in photosynthesis. Improvements in the enzyme would lead to an increase in the production of food, fiber, and renewable energy. Although the large subunit contains the active site, a family of rbcS nuclear genes encodes the Rubisco small subunits, which can also influence the carboxylation catalytic efficiency and CO₂/O₂ specificity of the enzyme. To further define the role of the small subunit in Rubisco function, small subunits from spinach, Arabidopsis, and sunflower were assembled with algal large subunits by transformation of a Chlamydomonas reinhardtii mutant that lacks the rbcS gene family. Foreign rbcS cDNAs were successfully expressed in Chlamydomonas by fusing them to a Chlamydomonas rbcS transit peptide sequence engineered to contain rbcS introns. Although plant Rubisco generally has greater CO₂/O₂ specificity but a lower carboxylation V_max than Chlamydomonas Rubisco, the hybrid enzymes have 3–11% increases in CO₂/O₂ specificity and retain near normal V_max values. Thus, small subunits may make a significant contribution to the overall catalytic performance of Rubisco. Despite having normal amounts of catalytically proficient Rubisco, the hybrid mutant strains display reduced levels of photosynthetic growth and lack chloroplast pyrenoids. It appears that small subunits contain the structural elements responsible for targeting Rubisco to the algal pyrenoid, which is the site where CO₂ is concentrated for optimal photosynthesis.     

From chaperonins to Rubisco assembly and metabolic repair

Ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) mediates the fixation of atmospheric CO₂ in photosynthesis by catalyzing the carboxylation of the 5‐carbon sugar ribulose‐1,5‐bisphosphate (RuBP). Despite its pivotal role, Rubisco is an inefficient enzyme and thus has been a key target for bioengineering. However, efforts to increase crop yields by Rubisco engineering remain unsuccessful, due in part to the complex machinery of molecular chaperones required for Rubisco biogenesis and metabolic repair. While the large subunit of Rubisco generally requires the chaperonin system for folding, the evolution of the hexadecameric Rubisco from its dimeric precursor resulted in the dependence on an array of additional factors required for assembly. Moreover, Rubisco function can be inhibited by a range of sugar‐phosphate ligands. Metabolic repair of Rubisco depends on remodeling by the ATP‐dependent Rubisco activase and hydrolysis of inhibitors by specific phosphatases. This review highlights our work toward understanding the structure and mechanism of these auxiliary machineries.     

In Vivo Studies in Rhodospirillum rubrum Indicate That Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Catalyzes Two Obligatorily Required and Physiologically Significant Reactions for Distinct Carbon and Sulfur Metabolic Pathways

All organisms possess fundamental metabolic pathways to ensure that needed carbon and sulfur compounds are provided to the cell in the proper chemical form and oxidation state. For most organisms capable of using CO₂ as sole source of carbon, ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) catalyzes primary carbon dioxide assimilation. In addition, sulfur salvage pathways are necessary to ensure that key sulfur-containing compounds are both available and, where necessary, detoxified in the cell. Using knock-out mutations and metabolomics in the bacterium Rhodospirillum rubrum, we show here that Rubisco concurrently catalyzes key and essential reactions for seemingly unrelated but physiologically essential central carbon and sulfur salvage metabolic pathways of the cell. In this study, complementation and mutagenesis studies indicated that representatives of all known extant functional Rubisco forms found in nature are capable of simultaneously catalyzing reactions required for both CO₂-dependent growth as well as growth using 5-methylthioadenosine as sole sulfur source under anaerobic photosynthetic conditions. Moreover, specific inactivation of the CO₂ fixation reaction did not affect the ability of Rubisco to support anaerobic 5-methylthioadenosine metabolism, suggesting that the active site of Rubisco has evolved to ensure that this enzyme maintains both key functions. Thus, despite the coevolution of both functions, the active site of this protein may be differentially modified to affect only one of its key functions.     

Activities of carboxylating enzymes in the CAM species Opuntia ficus-indica grown under current and elevated CO2 concentrations

Responses of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and phosphoenolpyruvate carboxylase (PEPCase) to an elevated atmospheric CO₂ concentration were determined along with net CO₂ uptake rates for the Crassulacean acid metabolism species Opuntia ficus-indica growing in open-top chambers. During the spring 13 months after planting, total daily net CO₂ uptake of basal and first-order daughter cladodes was 28% higher at 720 than at 360 l CO₂ l^-1. The enhancement, caused mainly by higher CO₂ assimilation during the early part of the night, was also observed during late summer (5 months after planting) and the following winter. The activities of Rubisco and PEPCase measured in vitro were both lower at the elevated CO₂ concentration, particularly under the more favorable growth conditions in the spring and late summer. Enzyme activity in second-order daughter cladodes increased with cladode age, becoming maximal at 6 to 10 days. The effect ofelevated CO₂ on Rubisco and PEPCase activity declined with decreasing irradiance, especially for Rubisco. Throughout the 13-month observation period, O. ficus-indica thus showed increased CO₂ uptake when the atmospheric CO₂ concentration was doubled despite lower activities of both carboxylating enzymes.     

Energy crosstalk between photosynthesis and the algal CO2-concentrating mechanisms

Microalgal photosynthesis is responsible for nearly half of the CO₂ annually captured by Earth’s ecosystems. In aquatic environments where the CO₂ availability is low, the CO₂-fixing efficiency of microalgae greatly relies on mechanisms – called CO_2-concentrating mechanisms (CCMs) – for concentrating CO₂ at the catalytic site of the CO₂-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). While the transport of inorganic carbon (C_i) across membrane bilayers against a concentration gradient consumes part of the chemical energy generated by photosynthesis, the bioenergetics and cellular mechanisms involved are only beginning to be elucidated. Here, we review the current knowledge relating to the energy requirement of CCMs in the light of recent advances in photosynthesis regulatory mechanisms and the spatial organization of CCM components.     

Variable mesophyll conductance revisited: theoretical background and experimental implications

The CO₂ concentration at the site of carboxylation inside the chloroplast stroma depends not only on the stomatal conductance, but also on the conductance of CO₂ between substomatal cavities and the site of CO₂ fixation. This conductance, commonly termed mesophyll conductance (g_m), significantly constrains the rate of photosynthesis. Here we show that estimates of g_m are influenced by the amount of respiratory and photorespiratory CO₂ from the mitochondria diffusing towards the chloroplasts. This results in an apparent CO₂ and oxygen sensitivity of g_m that does not imply a change in intrinsic diffusion properties of the mesophyll, but depends on the ratio of mitochondrial CO₂ release to chloroplast CO₂ uptake. We show that this effect (1) can bias the estimation of the CO₂ photocompensation point and non‐photorespiratory respiration in the light; (2) can affect the estimates of ribulose 1·5‐bisphosphate carboxylase/oxygenase (Rubisco) kinetic constants in vivo; and (3) results in an apparent obligatory correlation between stomatal conductance and g_m. We further show that the amount of photo(respiratory) CO₂ that is refixed by Rubisco can be directly estimated through measurements of g_m.     

Rubisco Evolution in C4 Eudicots: An Analysis of Amaranthaceae Sensu Lato

Background

Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO₂. In C₄ plants CO₂ is supplied to Rubisco by an auxiliary CO₂-concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C₄ Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C₃ enzyme. Specific amino-acids in Rubisco are associated with C₄ photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots.

Methodology/Principal Findings

We investigated Rubisco evolution in Amaranthaceae sensu lato (including Chenopodiaceae), the third-largest family of C₄ plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast rbcL gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C₄ Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C₄ plant groups, such as C₄ monocots, illustrating a striking parallelism in molecular evolution.

Conclusions/Significance

Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco.     

Determination of Apparent K(m) Values for Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Activase Using the Spectrophotometric Assay of Rubisco Activity

The spectrophotometric assay for ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) was used to determine the rate of increase in Rubisco activity over time in the presence or absence of Rubisco activase. Polynomial approximations to the raw data were used to smooth out minor fluctuations in the spectrophotometer readings, and Rubisco activase activity was expressed as nanomoles of activated Rubisco per minute. This assay was used to examine the effects of CO₂ and the inactive-Rubisco:ribulose 1,5-bisphosphate complex (ER) on the activase-catalyzed activation reaction. Double-reciprocal plots of activase activity and ER at several concentrations of CO₂ were consistent with two-substrate Michaelis-Menton kinetics, and the apparent K_m (CO₂) and K_m(ER) were determined to be 53 and 2.7 micromolar, respectively. These data do not prove that ER and CO₂ are substrates for the reaction catalyzed by activase, but they may be important to our understanding of the activation process in vivo. The implications of these data and their relation to previously published data on the effects of ER and CO₂ on activase are discussed.     

Effect of O2:CO2 ratio on the primary metabolism of Chlamydomonas reinhardtii

High oxygen:carbon dioxide ratios may have a negative effect on growth and productivity of microalgae. To investigate the effect of O₂ and CO₂ concentrations and the ratio between these on the metabolism of Chlamydomonas reinhardtii we performed turbidostat experiments at different O₂:CO₂ ratios. These experiments showed that elevated O₂ concentrations and the corresponding increase in the ratio of O₂:CO₂ common in photobioreactors led to a reduction of growth and biomass yield on light with 20–30%. This is most probably related to the oxygenase activity of Rubisco and the resulting process of photorespiration. Using metabolic flux modeling with measured rates for each experiment we were able to quantify the ratio of the oxygenase reaction to the carboxylase reaction of Rubisco and could demonstrate that photorespiration indeed can cause the reduction in biomass yield on light. The calculated ratio of the oxygenase reaction to the carboxylase reaction was 16.6% and 20.5% for air with 2% CO₂ and 1% CO₂, respectively. Thus photorespiration has a significant impact on the biomass yield on light already at conditions common in photobioreactors (air with 2% CO₂). Biotechnol. Bioeng. 2011;108: 2390–2402. © 2011 Wiley Periodicals, Inc.