Rubisco regulation: a role for inhibitors

Impact of the plastidial stringent response in plant growth and stress responses

The regulatory nucleotide guanosine 5'-diphosphate 3'-diphosphate (ppGpp), which was originally identified in Escherichia coli, controls the expression of a large gene set and many enzyme activities. The ppGpp-dependent control of cell activities is referred to as the stringent response. Recently, genes responsible for the synthesis and degradation of ppGpp have been identified not only in bacteria, but also in eukaryotes, including plants and animals, indicating that the stringent response is, unexpectedly, widely conserved. However, the exact function of the eukaryotic stringent response remains elusive. Here, we isolated an Arabidopsis mutant that overproduces ppGpp in chloroplasts. This mutant shows metabolite reduction, dwarf chloroplasts and significantly suppressed plastidial transcription and translation. Under nutrient-deficient conditions, the mutant shows more robust growth than the wild type. These results indicate that the ppGpp-dependent control of the organelle function is crucial for the systematic growth of host organisms.

Structural Characterization of a Newly Identified Component of α-Carboxysomes: The AAA+ Domain Protein CsoCbbQ

Carboxysomes are bacterial microcompartments that enhance carbon fixation by concentrating ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and its substrate CO2 within a proteinaceous shell. They are found in all cyanobacteria, some purple photoautotrophs and many chemoautotrophic bacteria. Carboxysomes consist of a protein shell that encapsulates several hundred molecules of RuBisCO, and contain carbonic anhydrase and other accessory proteins. Genes coding for carboxysome shell components and the encapsulated proteins are typically found together in an operon. The α-carboxysome operon is embedded in a cluster of additional, conserved genes that are presumably related to its function. In many chemoautotrophs, products of the expanded carboxysome locus include CbbO and CbbQ, a member of the AAA+ domain superfamily. We bioinformatically identified subtypes of CbbQ proteins and show that their genes frequently co-occur with both Form IA and Form II RuBisCO. The α-carboxysome-associated ortholog, CsoCbbQ, from Halothiobacillus neapolitanus forms a hexamer in solution and hydrolyzes ATP. The crystal structure shows that CsoCbbQ is a hexamer of the typical AAA+ domain; the additional C-terminal domain, diagnostic of the CbbQ subfamily, structurally fills the inter-monomer gaps, resulting in a distinctly hexagonal shape. We show that CsoCbbQ interacts with CsoCbbO and is a component of the carboxysome shell, the first example of ATPase activity associated with a bacterial microcompartment.

Optimizing Rubisco and its regulation for greater resource use efficiency

Rubisco catalyses the carboxylation of ribulose-1,5-bisphosphate (RuBP), enabling net CO2 assimilation in photosynthesis. The properties and regulation of Rubisco are not optimal for biomass production in current and projected future environments. Rubisco is relatively inefficient, and large amounts of the enzyme are needed to support photosynthesis, requiring large investments in nitrogen. The competing oxygenation of RuBP by Rubisco decreases photosynthetic efficiency. Additionally, Rubisco is inhibited by some sugar phosphates and depends upon interaction with Rubisco activase (Rca) to be reactivated. Rca activity is modulated by the chloroplast redox status and ADP/ATP ratios, thereby mediating Rubisco activation and photosynthetic induction in response to irradiance. The extreme thermal sensitivity of Rca compromises net CO2 assimilation at moderately high temperatures. Given its central role in carbon assimilation, the improvement of Rubisco function and regulation is tightly linked with irradiance, nitrogen and water use efficiencies. Although past attempts have had limited success, novel technologies and an expanding knowledge base make the challenge of improving Rubisco activity in crops an achievable goal. Strategies to optimize Rubisco and its regulation are addressed in relation to their potential to improve crop resource use efficiency and climate resilience of photosynthesis.

A reversible decrease in ribulose 1,5-bisphosphate carboxylase/oxygenase carboxylation activity caused by the aggregation of the enzyme's large subunit is triggered in response to the exposure of moderate irradiance-grown plants to low irradiance

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is highly regulated in response to fluctuations in the environment, including changes in irradiance. However, no complex data are available on Rubisco regulatory mechanisms triggered in plants which are submitted to moderate-low irradiance shift. Therefore, we investigated in a comprehensive way the changes at the level of amount of Rubisco protein, its structural organization and carboxylase activity of the holoenzyme as triggered by exposure of moderate irradiance-grown Arabidopsis thaliana plants to low irradiance conditions. An exposure of moderate irradiance-grown plants to low irradiance for a single photoperiod caused the exclusion of a certain pool of Rubisco under altered conditions owing to oxidative modifications resulting in the formation of protein aggregates involving Rubisco large subunit (LS). As a result, both initial and total Rubisco carboxylase activities were reduced, whereas Rubisco activation state remained largely unchanged. The results of the determination of reactive oxygen species indicated that a moderate/low irradiance transition had stimulated (1) O2 accumulation and we strongly suggest that Rubisco oxidative modifications leading to formation of aggregates encompassing Rubisco-LS were triggered by (1) O2 . When moderate irradiance regime was resumed, the majority of Rubisco-LS containing aggregates tended to be resolubilized, and this allowed Rubisco carboxylation activities to be largely recovered, without changes in the activation state of the enzyme. In the longer term, these results allow us to better understand a complexity of Rubisco regulatory mechanisms activated in response to abiotic stresses and during recovery from the stresses.

Identification of Interactions between Abscisic Acid and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase

Abscisic acid ((+)-ABA) is a phytohormone involved in the modulation of developmental processes and stress responses in plants. A chemical proteomics approach using an ABA mimetic probe was combined with in vitro assays, isothermal titration calorimetry (ITC), x-ray crystallography and in silico modelling to identify putative (+)-ABA binding-proteins in crude extracts of Arabidopsis thaliana. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was identified as a putative ABA-binding protein. Radiolabelled-binding assays yielded a K_d of 47 nM for (+)-ABA binding to spinach Rubisco, which was validated by ITC, and found to be similar to reported and experimentally derived values for the native ribulose-1,5-bisphosphate (RuBP) substrate. Functionally, (+)-ABA caused only weak inhibition of Rubisco catalytic activity (K_i of 2.1 mM), but more potent inhibition of Rubisco activation (K_i of ~ 130 μM). Comparative structural analysis of Rubisco in the presence of (+)-ABA with RuBP in the active site revealed only a putative low occupancy (+)-ABA binding site on the surface of the large subunit at a location distal from the active site. However, subtle distortions in electron density in the binding pocket and in silico docking support the possibility of a higher affinity (+)-ABA binding site in the RuBP binding pocket. Overall we conclude that (+)-ABA interacts with Rubisco. While the low occupancy (+)-ABA binding site and weak non-competitive inhibition of catalysis may not be relevant, the high affinity site may allow ABA to act as a negative effector of Rubisco activation.

Role of auxiliary proteins in Rubisco biogenesis and function

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the conversion of atmospheric CO2 into organic compounds during photosynthesis. Despite its pivotal role in plant metabolism, Rubisco is an inefficient enzyme and has therefore been a key target in bioengineering efforts to improve crop yields. Much has been learnt about the complex cellular machinery involved in Rubisco assembly and metabolic repair over recent years. The simple form of Rubisco found in certain bacteria and dinoflagellates comprises two large subunits, and generally requires the chaperonin system for folding. However, the evolution of hexadecameric Rubisco, which comprises eight large and eight small subunits, from its dimeric precursor has rendered Rubisco in most plants, algae, cyanobacteria and proteobacteria dependent on an array of additional factors. These auxiliary factors include several chaperones for assembly as well as ATPases of the AAA+ family for functional maintenance. An integrated view of the pathways underlying Rubisco biogenesis and repair will pave the way for efforts to improve the enzyme with the goal of increasing crop yields.

The HIV-1 Pr55 gag polyprotein binds to plastidial membranes and leads to severe impairment of chloroplast biogenesis and seedling lethality in transplastomic tobacco plants

Chloroplast genetic engineering has long been recognised as a powerful technology to produce recombinant proteins. To date, however, little attention has been given to the causes of pleiotropic effects reported, in some cases, as consequence of the expression of foreign proteins in transgenic plastids. In this study, we investigated the phenotypic alterations observed in transplastomic tobacco plants accumulating the Pr55(gag) polyprotein of human immunodeficiency virus (HIV-1). The expression of Pr55(gag) at high levels in the tobacco plastome leads to a lethal phenotype of seedlings grown in soil, severe impairment of plastid development and photosynthetic activity, with chloroplasts largely resembling undeveloped proplastids. These alterations are associated to the binding of Pr55(gag) to thylakoids. During particle assembly in HIV-1 infected human cells, the binding of Pr55(gag) to a specific lipid [phosphatidylinositol-(4-5) bisphosphate] in the plasma membrane is mediated by myristoylation at the amino-terminus and the so-called highly basic region (HBR). Surprisingly, the non-myristoylated Pr55(gag) expressed in tobacco plastids was likely able, through the HBR motif, to bind to nonphosphorous glycerogalactolipids or other classes of lipids present in plastidial membranes. Although secondary consequences of disturbed chloroplast biogenesis on expression of nuclear-encoded plastid proteins cannot be ruled out, results of proteomic analyses suggest that their altered accumulation could be due to retrograde control in which chloroplasts relay their status to the nucleus for fine-tuning of gene expression.

Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants

BACKGROUND

Crop plants such as rice, maize and sorghum play economically-important roles as main sources of food, fuel, and animal feed. However, current genome annotations of crop plants still suffer false-positive predictions; a more comprehensive registry of alternative splicing (AS) events is also in demand. Comparative genomics of crop plants is largely unexplored.

RESULTS

We performed a large-scale comparative analysis (ExonFinder) of the expressed sequence tag (EST) library from nine grass plants against three crop genomes (rice, maize, and sorghum) and identified 2,879 previously-unannotated exons (i.e., novel exons) in the three crops. We validated 81% of the tested exons by RT-PCR-sequencing, supporting the effectiveness of our in silico strategy. Evolutionary analysis reveals that the novel exons, comparing with their flanking annotated ones, are generally under weaker selection pressure at the protein level, but under stronger pressure at the RNA level, suggesting that most of the novel exons also represent novel alternatively spliced variants (ASVs). However, we also observed the consistency of evolutionary rates between certain novel exons and their flanking exons, which provided further evidence of their co-occurrence in the transcripts, suggesting that previously-annotated isoforms might be subject to erroneous predictions. Our validation showed that 54% of the tested genes expressed the newly-identified isoforms that contained the novel exons, rather than the previously-annotated isoforms that excluded them. The consistent results were steadily observed across cultivated (Oryza sativa and O. glaberrima) and wild (O. rufipogon and O. nivara) rice species, asserting the necessity of our curation of the crop genome annotations. Our comparative analyses also inferred the common ancestral transcriptome of grass plants and gain- and loss-of-ASV events.

CONCLUSIONS

We have reannotated the rice, maize, and sorghum genomes, and showed that evolutionary rates might serve as an indicator for determining whether the identified exons were alternatively spliced. This study not only presents an effective in silico strategy for the improvement of plant annotations, but also provides further insights into the role of AS events in the evolution and domestication of crop plants. ExonFinder and the novel exons/ASVs identified are publicly accessible at http://exonfinder.sourceforge.net/ .

Degradation of potent Rubisco inhibitor by selective sugar phosphatase

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the conversion of atmospheric carbon dioxide into organic compounds in photosynthetic organisms. Alongside carboxylating the five-carbon sugar ribulose-1,5-bisphosphate (RuBP)(1-3), Rubisco produces a small amount of xylulose-1,5-bisphosphate (XuBP), a potent inhibitor of Rubisco(4). The AAA+ protein Rubisco activase removes XuBP from the active site of Rubisco in an ATP-dependent process(5,6). However, free XuBP rapidly rebinds to Rubisco, perpetuating its inhibitory effect. Here, we combine biochemical and structural analyses to show that the CbbY protein of the photosynthetic bacterium Rhodobacter sphaeroides and Arabidopsis thaliana is a highly selective XuBP phosphatase. We also show that CbbY converts XuBP to the non-inhibitory compound xylulose-5-phosphate, which is recycled back to RuBP. We solve the crystal structures of CbbY from R. sphaeroides and A. thaliana, and through mutational analysis show that the cap domain of the protein confers the selectivity for XuBP over RuBP. Finally, in vitro experiments with CbbY from R. sphaeroides reveal that CbbY cooperates with Rubisco activase to prevent a detrimental build-up of XuBP at the Rubisco active site. We suggest that CbbY, which is conserved in algae and plants, is an important component of the cellular machinery that has evolved to deal with the shortcomings of the ancient enzyme Rubisco.

A faster Rubisco with potential to increase photosynthesis in crops

In photosynthetic organisms, D-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating atmospheric CO2 into the biosphere. Owing to the wasteful oxygenase activity and slow turnover of Rubisco, the enzyme is among the most important targets for improving the photosynthetic efficiency of vascular plants. It has been anticipated that introducing the CO2-concentrating mechanism (CCM) from cyanobacteria into plants could enhance crop yield. However, the complex nature of Rubisco's assembly has made manipulation of the enzyme extremely challenging, and attempts to replace it in plants with the enzymes from cyanobacteria and red algae have not been successful. Here we report two transplastomic tobacco lines with functional Rubisco from the cyanobacterium Synechococcus elongatus PCC7942 (Se7942). We knocked out the native tobacco gene encoding the large subunit of Rubisco by inserting the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35, which incorporates three small subunit-like domains. Se7942 Rubisco and CcmM35 formed macromolecular complexes within the chloroplast stroma, mirroring an early step in the biogenesis of cyanobacterial β-carboxysomes. Both transformed lines were photosynthetically competent, supporting autotrophic growth, and their respective forms of Rubisco had higher rates of CO2 fixation per unit of enzyme than the tobacco control. These transplastomic tobacco lines represent an important step towards improved photosynthesis in plants and will be valuable hosts for future addition of the remaining components of the cyanobacterial CCM, such as inorganic carbon transporters and the β-carboxysome shell proteins.

Evolutionary development of redox regulation in chloroplasts

SIGNIFICANCE

The post-translational modification of thiol groups stands out as a key strategy that cells employ for metabolic regulation and adaptation to changing environmental conditions. Nowhere is this more evident than in chloroplasts-the O2-evolving photosynthetic organelles of plant cells that are fitted with multiple redox systems, including the thioredoxin (Trx) family of oxidoreductases functional in the reversible modification of regulatory thiols of proteins in all types of cells. The best understood member of this family in chloroplasts is the ferredoxin-linked thioredoxin system (FTS) by which proteins are modified via light-dependent disulfide/dithiol (S-S/2SH) transitions.

RECENT ADVANCES

Discovered in the reductive activation of enzymes of the Calvin-Benson cycle in illuminated chloroplast preparations, recent studies have extended the role of the FTS far beyond its original boundaries to include a spectrum of cellular processes. Together with the NADP-linked thioredoxin reductase C-type (NTRC) and glutathione/glutaredoxin systems, the FTS also plays a central role in the response of chloroplasts to different types of stress.

CRITICAL ISSUES

The comparisons of redox regulatory networks functional in chloroplasts of land plants with those of cyanobacteria-prokaryotes considered to be the ancestors of chloroplasts-and different types of algae summarized in this review have provided new insight into the evolutionary development of redox regulation, starting with the simplest O2-evolving organisms.

FUTURE DIRECTIONS

The evolutionary appearance, mode of action, and specificity of the redox regulatory systems functional in chloroplasts, as well as the types of redox modification operating under diverse environmental conditions stand out as areas for future study.

The contribution of dynamic changes in photosynthesis to shade tolerance of two conifer species

Generally 'shade tolerance' refers to the capacity of a plant to exist at low light levels but characteristics of shade can vary and must be taken into account in defining the term. We studied Abies amabilis Dougl. ex J.Forbes and Tsuga heterophylla (Raf.) Sarg. under a forest canopy in the northwest of the Olympic Peninsula, USA, which has low annual sunshine hours and frequent overcast days. Using BF3 sunshine sensors, we surveyed diffuse and total light received by saplings growing under a range of canopy openness up to 30%. We measured variation in photosynthetic capacity over the growing season and within days and estimated photosynthesis induction in relation to ambient light. Three components of shade tolerance are associated with variation in light climate: (i) Total light on the floor of an 88-year stand of naturally regenerated T. heterophylla was greater on overcast than clear days. Light on overcast days varied throughout the day sometimes with a cyclical pattern. (ii) Photosynthetic capacity, Amax, varied both through the growing season and within days. Amax was generally greater in the latter part of the growing season, being limited by temperature and stomatal conductance, gs, at times during the early part. Saplings in more shaded areas had lower Amax and in the latter part of the growing season Amax was found to decline from mid-afternoon. (iii) Two patterns of photosynthesis induction to increased light were found. In a mean ambient light of 139 μmol m(-2) s(-1), induction had a curvilinear response to a step increase in light with a mean time constant, τ, of 112.3 s. In a mean ambient light of 74 μmol m(-2) s(-1), induction had a two-part increase: one with τ1 of 11.3 s and the other with τ2 of 184.0 s. These are the smallest published values of τ to date. (iv) Both variation in photosynthetic capacity and induction are components of shade tolerance where light varies over time. Amax acclimates to seasonal and diurnal changes in light and varies between microenvironments. The rapid induction processes can cause a rapid response of photosynthesis to changes in diffuse or direct light.

Structure-function studies with the unique hexameric form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Rhodopseudomonas palustris

The first x-ray crystal structure has been solved for an activated transition-state analog-bound form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). This enzyme, from Rhodopseudomonas palustris, assembles as a unique hexamer with three pairs of catalytic large subunit homodimers around a central 3-fold symmetry axis. This oligomer arrangement is unique among all known Rubisco structures, including the form II homolog from Rhodospirillum rubrum. The presence of a transition-state analog in the active site locked the activated enzyme in a "closed" conformation and revealed the positions of critical active site residues during catalysis. Functional roles of two form II-specific residues (Ile(165) and Met(331)) near the active site were examined via site-directed mutagenesis. Substitutions at these residues affect function but not the ability of the enzyme to assemble. Random mutagenesis and suppressor selection in a Rubisco deletion strain of Rhodobacter capsulatus identified a residue in the amino terminus of one subunit (Ala(47)) that compensated for a negative change near the active site of a neighboring subunit. In addition, substitution of the native carboxyl-terminal sequence with the last few dissimilar residues from the related R. rubrum homolog increased the enzyme's kcat for carboxylation. However, replacement of a longer carboxyl-terminal sequence with termini from either a form III or a form I enzyme, which varied both in length and sequence, resulted in complete loss of function. From these studies, it is evident that a number of subtle interactions near the active site and the carboxyl terminus account for functional differences between the different forms of Rubiscos found in nature.

Isolation and kinetic characterisation of hydrophobically distinct populations of form I Rubisco

BACKGROUND

Rubisco (Ribulose-1,5-bisphosphate carboxylase/oxygenase) is a Calvin Cycle enzyme involved in CO2 assimilation. It is thought to be a major cause of photosynthetic inefficiency, suffering from both a slow catalytic rate and lack of specificity due to a competing reaction with oxygen. Revealing and understanding the engineering rules that dictate Rubisco's activity could have a significant impact on photosynthetic efficiency and crop yield.

RESULTS

This paper describes the purification and characterisation of a number of hydrophobically distinct populations of Rubisco from both Spinacia oleracea and Brassica oleracea extracts. The populations were obtained using a novel and rapid purification protocol that employs hydrophobic interaction chromatography (HIC) as a form I Rubisco enrichment procedure, resulting in distinct Rubisco populations of expected enzymatic activities, high purities and integrity.

CONCLUSIONS

We demonstrate here that HIC can be employed to isolate form I Rubisco with purities and activities comparable to those obtained via ion exchange chromatography (IEC). Interestingly, and in contrast to other published purification methods, HIC resulted in the isolation of a number of hydrophobically distinct Rubisco populations. Our findings reveal a so far unaccounted diversity in the hydrophobic properties within form 1 Rubisco. By employing HIC to isolate and characterise Spinacia oleracea and Brassica oleracea, we show that the presence of these distinct Rubisco populations is not species specific, and we report for the first time the kinetic properties of Rubisco from Brassica oleracea extracts. These observations may aid future studies concerning Rubisco's structural and functional properties.

Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii

We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.

C3 photosynthesis in the desert plant Rhazya stricta is fully functional at high temperatures and light intensities

The C3 plant Rhazya stricta is native to arid desert environment zones, where it experiences daily extremes of heat, light intensity (PAR) and high vapour pressure deficit (VPD). We measured the photosynthetic parameters in R. stricta in its native environment to assess the mechanisms that permit it to survive in these extreme conditions. Infrared gas exchange analysis examined diel changes in assimilation (A), stomatal conductance (gs ) and transpiration (E) on mature leaves of R. stricta. A/ci analysis was used to determine the effect of temperature on carboxylation capacity (Vc,max ) and the light- and CO2 -saturated rate of photosynthesis (Amax ). Combined chlorophyll fluorescence and gas exchange light response curve analysis at ambient and low oxygen showed that both carboxylation and oxygenation of Rubisco acted as the major sinks for the end products of electron transport. Physiological analysis in conjunction with gene expression analysis suggested that there are two isoforms of Rubisco activase which may provide an explanation for the ability of R. stricta to maintain Rubisco function at high temperatures. The potential to exploit this ability to cope with extreme temperatures is discussed in the context of future crop improvement.

Maintaining photosynthetic CO2 fixation via protein remodelling: the Rubisco activases

The key photosynthetic, CO2-fixing enzyme Rubisco forms inactivated complexes with its substrate ribulose 1,5-bisphosphate (RuBP) and other sugar phosphate inhibitors. The independently evolved AAA+ proteins Rubisco activase and CbbX harness energy from ATP hydrolysis to remodel Rubisco complexes, facilitating release of these inhibitors. Here, we discuss recent structural and mechanistic advances towards the understanding of protein-mediated Rubisco activation. Both activating proteins appear to form ring-shaped hexameric arrangements typical for AAA+ ATPases in their functional form, but display very different regulatory and biochemical properties. Considering the thermolability of the plant enzyme, an improved understanding of the mechanism for Rubisco activation may help in developing heat-resistant plants adapted to the challenge of global warming.

RNA-Seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis Sp

The photosynthetic cyanobacterium, Synechocystis sp. strain 6803, is a potential platform for the production of various chemicals and biofuels. In this study, direct photosynthetic production of a biopolymer, polyhydroxyalkanoate (PHA), in genetically engineered Synechocystis sp. achieved as high as 14 wt%. This is the highest production reported in Synechocystis sp. under photoautotrophic cultivation conditions without the addition of a carbon source. The addition of acetate increased PHA accumulation to 41 wt%, and this value is comparable to the highest production obtained with cyanobacteria. Transcriptome analysis by RNA-seq coupled with real-time PCR was performed to understand the global changes in transcript levels of cells subjected to conditions suitable for photoautotrophic PHA biosynthesis. There was lower expression of most PHA synthesis-related genes in recombinant Synechocystis sp. with higher PHA accumulation suggesting that the concentration of these enzymes is not the limiting factor to achieving high PHA accumulation. In order to cope with the higher PHA production, cells may utilize enhanced photosynthesis to drive the product formation. Results from this study suggest that the total flux of carbon is the possible driving force for the biosynthesis of PHA and the polymerizing enzyme, PHA synthase, is not the only critical factor affecting PHA-synthesis. Knowledge of the regulation or control points of the biopolymer production pathways will facilitate the further use of cyanobacteria for biotechnological applications.

Evaluation of five peanut (Arachis hypogaea) genotypes to identify drought responsive mechanisms utilising candidate-gene approach

Drought can significantly limit yield and quality in peanut (Arachis hypogaea L.), depending on its timing, duration and severity. The objective of this study was to identify potential molecular mechanism(s) utilising a candidate-gene approach in five peanut genotypes with contrasting drought responses. An early season drought stress treatment was applied under environmentally controlled rain-out shelters. When water was completely withheld for 3 weeks, no physical differences were observed for treated plants compared with their fully irrigated counterparts as indicated by relative water content; however, yield, grades (total sound mature kernel, TSMK), specific leaf area, and leaf dry matter content showed significant differences. Comparing expression levels of candidate genes, 'C76-16' exhibited significantly higher levels for CuZnSOD, NsLTP and drought protein 1 week earlier compared to the other genotypes, followed by significantly lower levels for the same genes. This suggested an early recognition of drought in C76-16 followed by an acclimation response. Cultivar 'Georgia Green' showed different patterns of gene-expression than C76-16. AP-3, a susceptible genotype, showed generally lower levels of gene-expression than C76-16 and Georgia Green. Myo-inositol phosphate synthase gene-expression showed high levels in irrigated treatment, ranging from 4-fold for 08T-12 to 12-fold for Georgia Green, but were significantly inhibited in drought treatment after 2 weeks of drought and after recovery.

Variation in Rubisco content and activity under variable climatic factors

The main objective of the present review is to provide a compilation of published data of the effects of several climatic conditions on Rubisco, particularly its activity, state of activation, and concentration, and its influence on leaf gas exchange and photosynthesis. The environmental conditions analyzed include drought, salinity, heavy metals, growth temperature, and elevated [O3], [CO2], and ultraviolet-B irradiance. The results show conclusive evidence for a major negative effect on activity of Rubisco with increasing intensity of a range of abiotic stress factors. This decrease in the activity of Rubisco is associated with down-regulation of the activation state of the enzyme (e.g., by de-carbamylation and/or binding of inhibitory sugar phosphates) in response to drought or high temperature. On the contrary, the negative effects of low temperature, heavy metal stress (cadmium), ozone, and UV-B stress on Rubisco activity are associated with changes in the concentration of Rubisco. Notably, in response to all environmental factors, the regulation of in vivo CO2 assimilation rate was related to Rubisco in vitro parameters, either concentration and/or carboxylation, depending on the particular stress. The importance of the loss of Rubisco activity and its repercussion on plant photosynthesis are discussed in the context of climate change. It is suggested that decreased Rubisco activity will be a major effect induced by climate change, which will need to be considered in any prediction model on plant productivity in the near future.

Comparative proteomic analysis of the stolon cold stress response between the C4 perennial grass species Zoysia japonica and Zoysia metrella

Zoysiagrass, the most cold-tolerant grass among the warm-season turfgrasses, is often used as a model species for isolating cellular components related to cold stress. To understand the proteomic responses to cold stress in zoysiagrass stolons, we extracted stolon proteins from Zoysiajaponica, cv. Meyer (cold-tolerant) and Z. metrella, cv. Diamond (cold-sensitive), which were grown with or without cold treatment. Approximately 700 proteins were resolved on 2-DE gels, and 70 protein spots were differentially accumulated. We further observed that 45 of the identified proteins participate in 10 metabolic pathways and cellular processes. A significantly greater number of proteins accumulated in the Meyer than in the Diamond and 15 increased proteins were detected only in the Meyer cultivar under cold stress. Furthermore, we propose a cold stress-responsive protein network composed of several different functional components that exhibits a balance between reactive oxygen species (ROS) production and scavenging, accelerated protein biosynthesis and proteolysis, reduced protein folding, enhanced photosynthesis, abundant energy supply and enhanced biosynthesis of carbohydrates and nucleotides. Generally, the cold-tolerant Meyer cultivar showed a greater ROS scavenging ability, more abundant energy supply and increased photosynthesis and protein synthesis than did the cold-sensitive Diamond cultivar, which may partly explain why Meyer is more cold tolerant.

The Antarctic Chlamydomonas raudensis: an emerging model for cold adaptation of photosynthesis

Permanently cold habitats dominate our planet and psychrophilic microorganisms thrive in cold environments. Environmental adaptations unique to psychrophilic microorganisms have been thoroughly described; however, the vast majority of studies to date have focused on cold-adapted bacteria. The combination of low temperatures in the presence of light is one of the most damaging environmental stresses for a photosynthetic organism: in order to survive, photopsychrophiles (i.e. photosynthetic organisms adapted to low temperatures) balance temperature-independent reactions of light energy capture/transduction with downstream temperature-dependent metabolic processes such as carbon fixation. Here, we review research on photopsychrophiles with a focus on an emerging model organism, Chlamydomonas raudensis UWO241 (UWO241). UWO241 is a psychrophilic green algal species and is a member of the photosynthetic microbial eukaryote community that provides the majority of fixed carbon for ice-covered lake ecosystems located in the McMurdo Dry Valleys, Antarctica. The water column exerts a range of environmental stressors on the phytoplankton community that inhabits this aquatic ecosystem, including low temperatures, extreme shade of an unusual spectral range (blue-green), high salinity, nutrient deprivation and extremes in seasonal photoperiod. More than two decades of work on UWO241 have produced one of our most comprehensive views of environmental adaptation in a cold-adapted, photosynthetic microbial eukaryote.

Photosynthetic characterization of Rubisco transplantomic lines reveals alterations on photochemistry and mesophyll conductance

Improving Rubisco catalysis is considered a promising way to enhance C3-photosynthesis and photosynthetic water use efficiency (WUE) provided the introduced changes have little or no impact on other processes affecting photosynthesis such as leaf photochemistry or leaf CO2 diffusion conductances. However, the extent to which the factors affecting photosynthetic capacity are co-regulated is unclear. The aim of the present study was to characterize the photochemistry and CO2 transport processes in the leaves of three transplantomic tobacco genotypes expressing hybrid Rubisco isoforms comprising different Flaveria L-subunits that show variations in catalysis and differing trade-offs between the amount of Rubisco and its activation state. Stomatal conductance (g s) in each transplantomic tobacco line matched wild-type, while their photochemistry showed co-regulation with the variations in Rubisco catalysis. A tight co-regulation was observed between Rubisco activity and mesophyll conductance (g m) that was independent of g s thus producing plants with varying g m/g s ratios. Since the g m/g s ratio has been shown to positively correlate with intrinsic WUE, the present results suggest that altering photosynthesis by modifying Rubisco catalysis may also be useful for targeting WUE.

Features of evolutionarily conserved alternative splicing events between Brassica and Arabidopsis

Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or down-regulation of gene expression by transcript decay. The evolutionary conservation of AS events in plants is largely unexplored and only a small number of AS events have been identified as conserved between divergent species. We performed a large-scale analysis of cDNA data from Brassica and Arabidopsis to identify and further characterize conserved AS events. We identified 537 conserved AS events in 485 genes. Alternative donor and acceptor events are significantly overrepresented among conserved events, whereas intron retention and exon skipping events are underrepresented. Conserved AS events are significantly shorter, less likely to be in the 3'UTR, and they are enriched for genes whose products function in the chloroplast. AS modified a functional domain for about half of the genes with conserved events. We further characterized three genes with conserved AS events. This study identifies many AS events that are conserved between Brassica and Arabidopsis, revealing features of conserved AS events. Many of the conserved AS events may have important, but uncharacterized, functions.

Influence of exogenous application of glutathione on rubisco and rubisco activase in heavy metal-stressed tobacco plant grown in vitro

The effect of glutathione on the influences of heavy metals affecting rubisco and rubisco activase was studied in tobacco plants grown in vitro where the shoot explants of the tobacco plant cultured on MS medium under aseptic conditions and two explants were placed in the control, 0.1 mM GSH, 1 mM GSH, 0.2 mM Cd, 0.2 mM Cu, 0.2 mM Zn, and a mixture of Cd and GSH, Cu and GSH, Zn and GSH, respectively. The effect of GSH on the growth of the tobacco plant was minimal, but the heavy metals clearly retarded its growth. GSH recovered the growth retarded by heavy metals, and the concentration of GSH required to recover the growth differed depending on the heavy metals. The content of chlorophyll in the plant increased through GSH and Zn, and decreased through Cd and Cu. The chlorophyll content which decreased due to Cd and Cu was recovered by GSH, and the content which increased due to Zn was decreased by 1 mM GSH. The content of rubisco decreased due to GSH and heavy metals, and the content which decreased due to heavy metals was recovered by GSH, and when GSH was treated with Zn, the increased rate was maximum compared to other heavy metals. The activity of rubisco was increased due to GSH and heavy metals, and the activity increased by Cd and Zn decreased through GSH. In the case of Cu, the activity of GSH increased even more. There was no effect of GSH on the influences of heavy metals on the content and activity of rubisco activase. The activity of rubisco decreased by thiourea among six denaturing agents, and increased by l-cysteine, and in most cases the activity level was recorded as high. The activity of rubisco activase all decreased as a result of six denaturing agents, and the effect caused by EDTA and guanidine-HCl was the greatest, while the effect caused by l-cysteine and urea was minimal.

Reversible inhibition of CO2 fixation by ribulose 1,5-bisphosphate carboxylase/oxygenase through the synergic effect of arsenite and a monothiol

The activity of the photosynthetic carbon-fixing enzyme, ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), is partially inhibited by arsenite in the millimolar concentration range. However, micromolar arsenite can fully inhibit Rubisco in the presence of a potentiating monothiol such as cysteine, cysteamine, 2-mercaptoethanol or N-acetylcysteine, but not glutathione. Arsenite reacts specifically with the vicinal Cys172-Cys192 from the large subunit of Rubisco and with the monothiol to establish a ternary complex, which is suggested to be a trithioarsenical. The stability of the complex is strongly dependent on the nature of the monothiol. Enzyme activity is fully recovered through the disassembly of the complex after eliminating arsenite and/or the thiol from the medium. The synergic combination of arsenite and a monothiol acts also in vivo stopping carbon dioxide fixation in illuminated cultures of Chlamydomonas reinhardtii. Again, this effect may be reverted by washing the cells. However, in vivo inhibition does not result from the blocking of Rubisco since mutant strains carrying Rubiscos with Cys172 and/or Cys192 substitutions (which are insensitive to arsenite in vitro) are also arrested. This suggests the existence of a specific sensor controlling carbon fixation that is even more sensitive than Rubisco to the arsenite-thiol synergism.

Physio-biochemical and proteome analysis of chickpea in early phases of cold stress

Intensive and short-term strategies can aid in more rapid screening with informative and reliable results for long-term investigations under cold stress (CS). The integration of cellular analysis of chickpea during 0, 2, 4, 8, and 12h CS supplied us with novel possible responsive components and the possible interactions embedded inside, still remaining a Maze. Seedlings showed a biphasic pattern of responses over time. The transitory phase happened after 8h, when cells are presumably experiencing a new stage of responses and setting the stage for long-term adjustments. Physio-biochemical analysis confirmed the direct effect of fatty acids composition, lipoxygenase activity and antioxidant systems in cell responses under CS. Also, proteome results using MALDI-TOF-TOF and/or LC-MS/MS were able to differentiate changes in early phases of CS. Two-dimensional gel analysis results showed the possible targets of CS as mitochondria, chloroplast, organelle-nucleus communications, storage resources, stress and defense, protein degradation and signal transduction that confirmed the cell intended to re-establish a new homeostasis, in energy and primary metabolites to adapt to long-term CS. Here we propose a time course dynamic assessing multi-dimensional approaches for CS studies as one of the first studies in short-term treatment to progressively fill in the gaps between physio-biochemical and molecular events and touch the cell architecture for a better comprehension of the nature of plant stress response.

Effects of exogenous abscisic acid on carbohydrate metabolism and the expression levels of correlative key enzymes in winter wheat under low temperature

Two wheat (Triticum aestivum) cultivars, freeze-tolerant Dongnongdongmai 1 and freeze-sensitive Jimai 22, were used in this study. They were grown under field conditions, the leaves were sprayed with 1 × 10(-5) mol/L ABA and distilled water as control respectively at the three-true-leaf stage. Application of exogenous ABA increased the accumulation of carbohydrates in both cultivars, mainly in sucrose and fructose, except that the fructose content decreased in the leaves of Jimai 22. Exogenous ABA also enhanced the expression of key enzyme genes, especially in Dongnongdongmai 1 above 0 °C and in Jimai 22 below 0 °C. The carbohydrate contents and expression levels of the genes encoding key enzymes showed co-regulation in some, but not all of the pathways examined. Taken together, the higher sugar accumulation and the upregulation in expression of key enzymes in freeze-tolerant Dongnongdongmai 1 due to exogenous ABA suggest that active carbohydrate metabolism is mainly associated with the freeze tolerance of Dongnongdongmai 1.

Rubisco activity and regulation as targets for crop improvement

Rubisco (ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase) enables net carbon fixation through the carboxylation of RuBP. However, some characteristics of Rubisco make it surprisingly inefficient and compromise photosynthetic productivity. For example, Rubisco catalyses a wasteful reaction with oxygen that leads to the release of previously fixed CO(2) and NH(3) and the consumption of energy during photorespiration. Furthermore, Rubisco is slow and large amounts are needed to support adequate photosynthetic rates. Consequently, Rubisco has been studied intensively as a prime target for manipulations to 'supercharge' photosynthesis and improve both productivity and resource use efficiency. The catalytic properties of Rubiscos from diverse sources vary considerably, suggesting that changes in turnover rate, affinity, or specificity for CO(2) can be introduced to improve Rubisco performance in specific crops and environments. While attempts to manipulate plant Rubisco by nuclear transformation have had limited success, modifying its catalysis by targeted changes to its catalytic large subunit via chloroplast transformation have been much more successful. However, this technique is still in need of development for most major food crops including maize, wheat, and rice. Other bioengineering approaches for improving Rubisco performance include improving the activity of its ancillary protein, Rubisco activase, in addition to modulating the synthesis and degradation of Rubisco's inhibitory sugar phosphate ligands. As the rate-limiting step in carbon assimilation, even modest improvements in the overall performance of Rubisco pose a viable pathway for obtaining significant gains in plant yield, particularly under stressful environmental conditions.

Elevated CO2 differentially affects photosynthetic induction response in two Populus species with different stomatal behavior

To understand dynamic photosynthetic characteristics in response to fluctuating light under a high CO(2) environment, we examined photosynthetic induction in two poplar genotypes from two species, Populus koreana 9 trichocarpa cv. Peace and Populus euramericana cv. I-55, respectively. Stomata of cv. Peace barely respond to changes in photosynthetic photon flux density (PFD), whereas those of cv. I-55 show a normal response to variations in PFD at ambient CO(2). The plants were grown under three CO2 regimes (380, 700, and 1,020 μmol CO(2) mol(-1) in air) for approximately 2 months. CO2 gas exchange was measured in situ in the three CO2 regimes under a sudden PFD increase from 20 to 800 μmol m(-2) s(-1). In both genotypes, plants grown under higher CO(2) conditions had a higher photosynthetic induction state, shorter induction time, and reduced induction limitation to photosynthetic carbon gain. Plants of cv. I-55 showed a much larger increase in induction state and decrease in induction time under high CO(2) regimes than did plants of cv. Peace. These showed that, throughout the whole induction process, genotype cv. I-55 had a much smaller reduction of leaf carbon gain under the two high CO(2) regimes than under the ambient CO(2) regime, while the high CO(2) effect was smaller in genotype cv. Peace. The results suggest that a high CO(2) environment can reduce both biochemical and stomatal limitations of leaf carbon gain during the photosynthetic induction process, and that a rapid stomatal response can further enhance the high CO(2) effect.

Effect of elevated carbon dioxide concentration on carbon assimilation under fluctuating light

Natural fluctuations in light intensity may significantly affect the amount of CO assimilated by plants and ecosystems. Little is known, however, about the interactive effect of dynamic light conditions and atmospheric CO concentrations. The hypothesis that elevated CO concentration (EC; 700 μmol CO mol) increases photosynthetic efficiency in dynamic light environments as compared to ambient CO concentration (AC; 385 μmol CO mol) was tested. Sun leaves of European beech ( L.) and current-year shoots of Norway spruce [ (L). Karst.] were exposed to five dynamic light regimes (LRs) occurring within forest canopies due to variable cloud cover or self-shading of leaves and to a steady-state LR. The LRs differed in the time course of incident irradiance, whereas the overall duration (600 s) and total amount of radiation (35.88 mmol photons m) were the same in all LRs. The EC treatment enhanced the amount of CO assimilated under all LRs tested. While the stimulation was only 37 to 50% in beech, it was 52 to 85% in spruce. The hypothesis that photosynthetic efficiency is stimulated by EC was confirmed in LRs when the leaves were pre-exposed to low light intensity and photosynthetic induction was required. By contrast, only a minor effect of EC treatment was found on the rate of induction loss and postillumination CO fixation in both species studied.

Rubisco activase is a key regulator of non-steady-state photosynthesis at any leaf temperature and, to a lesser extent, of steady-state photosynthesis at high temperature

The role of Rubisco activase in steady-state and non-steady-state photosynthesis was analyzed in wild-type (Oryza sativa) and transgenic rice that expressed different amounts of Rubisco activase. Below 25°C, the Rubisco activation state and steady-state photosynthesis were only affected when Rubisco activase was reduced by more than 70%. However, at 40°C, smaller reductions in Rubisco activase content were linked to a reduced Rubisco activation state and steady-state photosynthesis. As a result, overexpression of maize Rubisco activase in rice did not lead to an increase of the Rubisco activation state, nor to an increase in photosynthetic rate below 25°C, but had a small stimulatory effect at 40°C. On the other hand, the rate at which photosynthesis approached the steady state following an increase in light intensity was rapid in Rubisco activase-overexpressing plants, intermediate in the wild-type, and slowest in antisense plants at any leaf temperature. In Rubisco activase-overexpressing plants, Rubisco activation state at low light was maintained at higher levels than in the wild-type. Thus, rapid regulation by Rubisco activase following an increase in light intensity and/or maintenance of a high Rubisco activation state at low light would result in a rapid increase in Rubisco activation state and photosynthetic rate following an increase in light intensity. It is concluded that Rubisco activase plays an important role in the regulation of non-steady-state photosynthesis at any leaf temperature and, to a lesser extent, of steady-state photosynthesis at high temperature.

Effect of season, needle age and elevated CO2 concentration on photosynthesis and Rubisco acclimation in Picea abies

While downward photosynthetic acclimation in response to elevated CO(2) (EC) is frequently accompanied by reduction in Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), the exact mechanism behind this decrease and its dynamics are not well understood. We comprehensively studied Rubisco adjustment to EC in coniferous Picea abies using an electrophoretic (protein content), spectrophotometric (initial (RA(initial)) and total (RA(total)) in vitro Rubisco activities), and gas-exchange (maximum carboxylation activity in vivo (V(Cmax))) techniques. With respect to differing carbon sink strength and nitrogen remobilization, we hypothesized greater acclimation of photosynthesis in one-year-old as compared to current-year needles and at the end than at the beginning of the vegetation season. EC treatment led to a decrease in V(Cmax) values in current-year needles, but the ribulose-1,5-bisphosphate (RuBP)-limited rate of photosynthesis (J(max)) remained unaffected. Indeed, both V(Cmax) and J(max) were reduced by the EC treatment in one-year-old needles. The extent of photosynthetic acclimation in EC plants did not increase, however, during the vegetation season. EC decreased the activation state of Rubisco (RA(initial)/RA(total)) by 16% and 5% in current-year and one-year-old needles, respectively (averaged over the growing season). While during spring (short-term effect) EC treatment did not influence the Rubisco content per unit leaf area and decreased its specific activity (activity per unit Rubisco mass) in both needle age classes studied, exposure to EC during the entire vegetation season tended to reduce the Rubisco content while increasing its specific activity. Irrespective of CO(2) treatment and needle age, a hyperbolic-decay relationship was observed between Rubisco-specific activity and its content.

Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate

The key enzyme of plant photosynthesis, D-ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), must be activated to become catalytically competent via the carbamylation of Lys201 of the large subunit and subsequent stabilization by Mg(2+) coordination. Many biochemical studies have reported that reduced nicotinamide adenine dinucleotide phosphate (NADPH) and 6-phosphogluconate (6PG) function as positive effectors to promote activation. However, the structural mechanism remains unknown. Here, we have determined the crystal structures of activated rice Rubisco in complex with NADPH, 6PG, or 2-carboxy-D-arabinitol 1,5-bisphosphate (2CABP). The structures of the NADPH and 6PG complexes adopt open-state conformations, in which loop 6 at the catalytic site and some other loops are disordered. The structure of the 2CABP complex is in a closed state, similar to the previous 2CABP-bound activated structures from other sources. The catalytic sites of the NADPH and 6PG complexes are fully activated, despite the fact that bicarbonate (NaHCO(3)) was not added into the crystallization solution. In the catalytic site, NADPH does not interact with Mg(2+) directly but interacts with Mg(2+)-coordinated water molecules, while 6PG interacts with Mg(2+) directly. These observations suggest that the two effectors promote Rubisco activation by stabilizing the complex of Mg(2+) and the carbamylated Lys201 with unique interactions and preventing its dissociation. The structure also reveals that the relaxed complex of the effectors (NADPH or 6PG), distinct from the tight-binding mode of 2CABP, would allow rapid exchange of the effectors in the catalytic sites by substrate D-ribulose 1,5-bisphosphate for catalysis in physiological conditions.

2-Carboxy-D-arabinitol 1-phosphate (CA1P) phosphatase: evidence for a wider role in plant Rubisco regulation

The genes for CA1Pase (2-carboxy-D-arabinitol-1-bisphosphate phosphatase) from French bean, wheat, Arabidopsis and tobacco were identified and cloned. The deduced protein sequence included an N-terminal motif identical with the PGM (phosphoglycerate mutase) active site sequence [LIVM]-x-R-H-G-[EQ]-x-x-[WN]. The corresponding gene from wheat coded for an enzyme with the properties published for CA1Pase. The expressed protein lacked PGM activity but rapidly dephosphorylated 2,3-DPG (2,3-diphosphoglycerate) to 2-phosphoglycerate. DTT (dithiothreitol) activation and GSSG inactivation of this enzyme was pH-sensitive, the greatest difference being apparent at pH 8. The presence of the expressed protein during in vitro measurement of Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) activity prevented a progressive decline in Rubisco turnover. This was due to the removal of an inhibitory bisphosphate that was present in the RuBP (ribulose-1,5-bisphosphate) preparation, and was found to be PDBP (D-glycero-2,3-pentodiulose-1,5-bisphosphate). The substrate specificity of the expressed protein indicates a role for CA1Pase in the removal of 'misfire' products of Rubisco.

Structure of green-type Rubisco activase from tobacco

Rubisco, the enzyme that catalyzes the fixation of atmospheric CO(2) in photosynthesis, is subject to inactivation by inhibitory sugar phosphates. Here we report the 2.95-Å crystal structure of Nicotiana tabacum Rubisco activase (Rca), the enzyme that facilitates the removal of these inhibitors. Rca from tobacco has a classical AAA(+)-protein domain architecture. Although Rca populates a range of oligomeric states when in solution, it forms a helical arrangement with six subunits per turn when in the crystal. However, negative-stain electron microscopy of the active mutant R294V suggests that Rca functions as a hexamer. The residues determining species specificity for Rubisco are located in a helical insertion of the C-terminal domain and probably function in conjunction with the N-domain in Rubisco recognition. Loop segments exposed toward the central pore of the hexamer are required for the ATP-dependent remodeling of Rubisco, resulting in the release of inhibitory sugar.

Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase

Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the fixation of atmospheric CO(2) in photosynthesis, but tends to form inactive complexes with its substrate ribulose 1,5-bisphosphate (RuBP). In plants, Rubisco is reactivated by the AAA(+) (ATPases associated with various cellular activities) protein Rubisco activase (Rca), but no such protein is known for the Rubisco of red algae. Here we identify the protein CbbX as an activase of red-type Rubisco. The 3.0-Å crystal structure of unassembled CbbX from Rhodobacter sphaeroides revealed an AAA(+) protein architecture. Electron microscopy and biochemical analysis showed that ATP and RuBP must bind to convert CbbX into functionally active, hexameric rings. The CbbX ATPase is strongly stimulated by RuBP and Rubisco. Mutational analysis suggests that CbbX functions by transiently pulling the carboxy-terminal peptide of the Rubisco large subunit into the hexamer pore, resulting in the release of the inhibitory RuBP. Understanding Rubisco activation may facilitate efforts to improve CO(2) uptake and biomass production by photosynthetic organisms.

The activity of Rubisco's molecular chaperone, Rubisco activase, in leaf extracts

Rubisco frequently undergoes unproductive interactions with its sugar-phosphate substrate that stabilize active sites in an inactive conformation. Restoring catalytic competence to these sites requires the "molecular chiropractic" activity of Rubisco activase (activase). To make the study of activase more routine and physiologically relevant, an assay was devised for measuring activase activity in leaf extracts based on the ATP-dependent activation of inactive Rubisco. Control experiments with an Arabidopsis activase-deficient mutant confirmed that the rate of Rubisco activation was dependent on the concentration of activase in the extracts. Activase catalyzed Rubisco activation at rates equivalent to 9-14% catalytic sites per min in desalted extracts of Arabidopsis, camelina, tobacco, cotton, and wheat. Faster rates were observed in a transgenic line of Arabidopsis that expresses only the β-isoform of activase, whereas no activity was detected in a line that expresses only the α-isoform. Activase activity was also low or undetectable in rice, maize, and Chlamydomonas, revealing differences in the stability of the enzyme in different species. These differences are discussed in terms of the ability of activase subunits to remain associated or to reassociate into active oligomers when the stromal milieu is diluted by extraction. Finally, the temperature response of activase activity in leaf extracts differed for Arabidopsis, camelina, tobacco, and cotton, corresponding to the respective temperature responses of photosynthesis for each species. These results confirmed the exceptional thermal lability of activase at physiological ratios of activase to Rubisco.

Comparative proteomics analysis of salt response reveals sex-related photosynthetic inhibition by salinity in Populus cathayana cuttings

Male and female poplar ( Populus cathayana Rehd.) cuttings respond differently to salinity stress. To understand these differences better, comparative morphological, physiological, and proteomics analyses were performed. Treatments with different concentrations of NaCl applied to male and female poplar cuttings for 4 weeks showed that females reacted more negatively at the morphological and physiological levels than did males, visible as shriveled leaves, decreased growth, lowered photosynthetic capacities, and greater Na(+) accumulation. The proteome analysis identified 73 proteins from 82 sexually related salt-responsive spots. They were involved in photosynthesis, protein folding and assembly, synthesis and degradation, carbon, energy and steroid metabolism, plant stress and defense, redox homeostasis, signal transduction, and so forth. The sex-related changes of these proteins were consistent with the different morphological and physiological responses in males and females. In conclusion, the higher salt resistance of male P. cathayana cuttings is related to higher expression and lower degradation of proteins in the photosynthetic apparatus, more effective metabolic mechanism and protective system, and greater capacity of hydrogen peroxide scavenging. This research allows us to further understand the possible different management strategies of cellular activities in male and female Populus when confronted by salt stress.

Does ear C sink strength contribute to overcoming photosynthetic acclimation of wheat plants exposed to elevated CO2?

Wheat plants (Triticum durum Desf., cv. Regallo) were grown in the field to study the effects of contrasting [CO(2)] conditions (700 versus 370 μmol mol(-1)) on growth, photosynthetic performance, and C management during the post-anthesis period. The aim was to test whether a restricted capacity of sink organs to utilize photosynthates drives a loss of photosynthetic capacity in elevated CO(2). The ambient (13)C/(12)C isotopic composition (δ(13)C) of air CO(2) was changed from -10.2‰ in ambient [CO(2)] to -23.6‰ under elevated [CO(2)] between the 7th and the 14th days after anthesis in order to study C assimilation and partitioning between leaves and ears. Elevated [CO(2)] had no significant effect on biomass production and grain filling, and caused an accumulation of C compounds in leaves. This was accompanied by up-regulation of phosphoglycerate mutase and ATP synthase protein content, together with down-regulation of adenosine diphosphate glucose pyrophosphatase protein. Growth in elevated [CO(2)] negatively affected Rubisco and Rubisco activase protein content and induced photosynthetic down-regulation. CO(2) enrichment caused a specific decrease in Rubisco content, together with decreases in the amino acid and total N content of leaves. The C labelling revealed that in flag leaves, part of the C fixed during grain filling was stored as starch and structural C compounds whereas the rest of the labelled C (mainly in the form of soluble sugars) was completely respired 48 h after the end of labelling. Although labelled C was not detected in the δ(13)C of ear total organic matter and respired CO(2), soluble sugar δ(13)C revealed that a small amount of labelled C reached the ear. The (12)CO(2) labelling suggests that during the beginning of post-anthesis the ear did not contribute towards overcoming flag leaf carbohydrate accumulation, and this had a consequent effect on protein expression and photosynthetic acclimation.

Identification of differentially expressed genes in dormant (banjhi) bud of tea (Camellia sinensis (L.) O. Kuntze) using subtractive hybridization approach

Growth regulation associated with dormancy is an essential element in plant's life cycle that leads to changes in expression of large number of genes. Forward and reverse suppression subtractive hybridization (SSH) libraries were developed to identify and characterize the genes associated with bud (banjhi) dormancy in tea (Camellia sinensis (L.) O. Kuntze). Efficiency of subtraction was confirmed by comparing the abundance of β-actin gene. A total of 17 and 45 unique sequences were obtained from forward and reverse SSH library respectively. Many of the differentially regulated genes have unknown (41.1% and 26.7%) or hypothetical functions (11.7% and 2.2%) in forward and reverse SSH library respectively, while others have a role in cell growth and metabolism. Further, semi-quantitative RT-PCR was carried out for selected genes to validate the quality of ESTs from SSH library. Gene Ontology analysis identified a greater association of these ESTs in cellular metabolic pathways and their relevance to bud dormancy. Based on the EST data, the putative role of identified genes from tea is discussed in relation to dormancy, which includes various metabolic and signalling pathways. We demonstrated that SSH is an efficient tool for enriching up- and down-regulated genes related to bud dormancy in tea. This study represents an attempt to investigate banjhi dormancy in tea under field conditions, and the findings indicate that there is a potential to develop new approaches to modulate dormancy in this species.

The rate-limiting step for CO(2) assimilation at different temperatures is influenced by the leaf nitrogen content in several C(3) crop species

Effects of nitrogen (N) supply on the limiting step of CO(2) assimilation rate (A) at 380 µmol mol(-1) CO(2) concentration (A(380) ) at several leaf temperatures were studied in several crops, since N nutrition alters N allocation between photosynthetic components. Contents of leaf N, ribulose 1·5-bisphosphate carboxylase/oxygenase (Rubisco) and cytochrome f (cyt f) increased with increasing N supply, but the cyt f/Rubisco ratio decreased. Large leaf N content was linked to a high stomatal (g(s) ) and mesophyll conductance (g(m) ), but resulted in a lower intercellular (C(i) ) and chloroplast CO(2) concentration (C(c) ) because the increase in g(s) and g(m) was insufficient to compensate for change in A(380) . The A-C(c) response was used to estimate the maximum rate of RuBP carboxylation (V(cmax) ) and chloroplast electron transport (J(max) ). The J(max) /V(cmax) ratio decreased with reductions in leaf N content, which was consistent with the results of the cyt f/Rubisco ratio. Analysis using the C(3) photosynthesis model indicated that A(380) tended to be limited by RuBP carboxylation in plants grown at low N concentration, whereas it was limited by RuBP regeneration in plants grown at high N concentration. We conclude that the limiting step of A(380) depends on leaf N content and is mainly determined by N partitioning between Rubisco and electron transport components.

Raising yield potential of wheat. II. Increasing photosynthetic capacity and efficiency

Past increases in yield potential of wheat have largely resulted from improvements in harvest index rather than increased biomass. Further large increases in harvest index are unlikely, but an opportunity exists for increasing productive biomass and harvestable grain. Photosynthetic capacity and efficiency are bottlenecks to raising productivity and there is strong evidence that increasing photosynthesis will increase crop yields provided that other constraints do not become limiting. Even small increases in the rate of net photosynthesis can translate into large increases in biomass and hence yield, since carbon assimilation is integrated over the entire growing season and crop canopy. This review discusses the strategies to increase photosynthesis that are being proposed by the wheat yield consortium in order to increase wheat yields. These include: selection for photosynthetic capacity and efficiency, increasing ear photosynthesis, optimizing canopy photosynthesis, introducing chloroplast CO(2) pumps, increasing RuBP regeneration, improving the thermal stability of Rubisco activase, and replacing wheat Rubisco with that from other species with different kinetic properties.

Rubisco activity in Mediterranean species is regulated by the chloroplastic CO2 concentration under water stress

Water stress decreases the availability of the gaseous substrate for ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) by decreasing leaf conductance to CO(2). In spite of limiting photosynthetic carbon assimilation, especially in those environments where drought is the predominant factor affecting plant growth and yield, the effects of water deprivation on the mechanisms that control Rubisco activity are unclear. In the present study, 11 Mediterranean species, representing different growth forms, were subject to increasing levels of drought stress, the most severe one followed by rewatering. The results confirmed species-specific patterns in the decrease in the initial activity and activation state of Rubisco as drought stress and leaf dehydration intensified. Nevertheless, all species followed roughly the same trend when Rubisco activity was related to stomatal conductance (g(s)) and chloroplastic CO(2) concentration (C(c)), suggesting that deactivation of Rubisco sites could be induced by low C(c), as a result of water stress. The threshold level of C(c) that triggered Rubisco deactivation was dependent on leaf characteristics and was related to the maximum attained for each species under non-stressing conditions. Those species adapted to low C(c) were more capable of maintaining active Rubisco as drought stress intensified.

Plant physiology and proteomics reveals the leaf response to drought in alfalfa (Medicago sativa L.)

Despite its relevance, protein regulation, metabolic adjustment, and the physiological status of plants under drought is not well understood in relation to the role of nitrogen fixation in nodules. In this study, nodulated alfalfa plants were exposed to drought conditions. The study determined the physiological, metabolic, and proteomic processes involved in photosynthetic inhibition in relation to the decrease in nitrogenase (N(ase)) activity. The deleterious effect of drought on alfalfa performance was targeted towards photosynthesis and N(ase) activity. At the leaf level, photosynthetic inhibition was mainly caused by the inhibition of Rubisco. The proteomic profile and physiological measurements revealed that the reduced carboxylation capacity of droughted plants was related to limitations in Rubisco protein content, activation state, and RuBP regeneration. Drought also decreased amino acid content such as asparagine, and glutamic acid, and Rubisco protein content indicating that N availability limitations were caused by N(ase) activity inhibition. In this context, drought induced the decrease in Rubisco binding protein content at the leaf level and proteases were up-regulated so as to degrade Rubisco protein. This degradation enabled the reallocation of the Rubisco-derived N to the synthesis of amino acids with osmoregulant capacity. Rubisco degradation under drought conditions was induced so as to remobilize Rubisco-derived N to compensate for the decrease in N associated with N(ase) inhibition. Metabolic analyses showed that droughted plants increased amino acid (proline, a major compound involved in osmotic regulation) and soluble sugar (D-pinitol) levels to contribute towards the decrease in osmotic potential (Ψ(s)). At the nodule level, drought had an inhibitory effect on N(ase) activity. This decrease in N(ase) activity was not induced by substrate shortage, as reflected by an increase in total soluble sugars (TSS) in the nodules. Proline accumulation in the nodule could also be associated with an osmoregulatory response to drought and might function as a protective agent against ROS. In droughted nodules, the decrease in N(2) fixation was caused by an increase in oxygen resistance that was induced in the nodule. This was a mechanism to avoid oxidative damage associated with reduced respiration activity and the consequent increase in oxygen content. This study highlighted that even though drought had a direct effect on leaves, the deleterious effects of drought on nodules also conditioned leaf responsiveness.