The mechanisms of nitrogen assimilation in Pseudomonads

Pseudomonas aeruginosa, Ps. fluorescens and 3 marine psychrophylic pseudomonads were grown in chemostat cultures with nitrate ammonia or glutamate as nitrogen source. In cultures grown on nitrate (either carbon- or nitrogen-limited) and in ammonia nitrogen-limited cultures ammonia was assimilated via the GS/GOGAT pathway. With a excess of ammonia in the culture however ammonia was assimilated via GDH and GS was either present only at low levels or absent. Two distinct GDH activities were detected in all 5 bacteria, one specific to NAD and one to NADP. The presence of these activities was determined by the environment in which cells were grown. These activities showed differences with respect to substrate affinity (Km values) for ammonia, incubation temperature and to a lesser extent pH and may involve separate GDH isoenzymes. GS from the marine bacterium PL₁ had a very high affinity for ammonia (Km of 0.3mm) but a low affinity for glutamate (Km of 19mm).     

Role of carboxysomes in cyanobacterial CO2 assimilation: CO2 concentrating mechanisms and metabolon implications

Many carbon-fixing organisms have evolved CO₂ concentrating mechanisms (CCMs) to enhance the delivery of CO₂ to RuBisCO, while minimizing reactions with the competitive inhibitor, molecular O₂. These distinct types of CCMs have been extensively studied using genetics, biochemistry, cell imaging, mass spectrometry, and metabolic flux analysis. Highlighted in this paper, the cyanobacterial CCM features a bacterial microcompartment (BMC) called ‘carboxysome’ in which RuBisCO is co-encapsulated with the enzyme carbonic anhydrase (CA) within a semi-permeable protein shell. The cyanobacterial CCM is capable of increasing CO₂ around RuBisCO, leading to one of the most efficient processes known for fixing ambient CO₂. The carboxysome life cycle is dynamic and creates a unique subcellular environment that promotes activity of the Calvin–Benson (CB) cycle. The carboxysome may function within a larger cellular metabolon, physical association of functionally coupled proteins, to enhance metabolite channelling and carbon flux. In light of CCMs, synthetic biology approaches have been used to improve enzyme complex for CO₂ fixations. Research on CCM-associated metabolons has also inspired biologists to engineer multi-step pathways by providing anchoring points for enzyme cascades to channel intermediate metabolites towards valuable products.     

Silencing of OsCV (chloroplast vesiculation) maintained photorespiration and N assimilation in rice plants grown under elevated CO2

High CO₂ concentrations stimulate net photosynthesis by increasing CO₂ substrate availability for Rubisco, simultaneously suppressing photorespiration. Previously, we reported that silencing the chloroplast vesiculation (cv) gene in rice increased source fitness, through the maintenance of chloroplast stability and the expression of photorespiration-associated genes. Because high atmospheric CO₂ conditions diminished photorespiration, we tested whether CV silencing might be a viable strategy to improve the effects of high CO₂ on grain yield and N assimilation in rice. Under elevated CO₂, OsCV expression was induced, and OsCV was targeted to peroxisomes where it facilitated the removal of OsPEX11-1 from the peroxisome and delivered it to the vacuole for degradation. This process correlated well with the reduction in the number of peroxisomes, the decreased catalase activity and the increased H₂O₂ content in wild-type plants under elevated CO₂. At elevated CO₂, CV-silenced rice plants maintained peroxisome proliferation and photorespiration and displayed higher N assimilation than wild-type plants. This was supported by higher activity of enzymes involved in NO₃⁻ and NH₄⁺ assimilation and higher total and seed protein contents. Co-immunoprecipitation of OsCV-interacting proteins suggested that, similar to its role in chloroplast protein turnover, OsCV acted as a scaffold, binding peroxisomal proteins.     

Responses of the chloroplast glyoxalase system to high CO2 concentrations

ABSTRACT

Sugar metabolism pathways such as photosynthesis produce dicarbonyls, e.g. methylglyoxal (MG), which can cause cellular damage. The glyoxalase (GLX) system comprises two enzymes GLX1 and GLX2, and detoxifies MG; however, this system is poorly understood in the chloroplast, compared with the cytosol. In the present study, we determined GLX1 and GLX2 activities in spinach chloroplasts, which constituted 40% and 10%, respectively, of the total leaf glyoxalase activity. In Arabidopsis thaliana, five GFP-fusion GLXs were present in the chloroplasts. Under high CO₂ concentrations, where increased photosynthesis promotes the MG production, GLX1 and GLX2 activities in A. thaliana increased and the expression of AtGLX1-2 and AtGLX2-5 was enhanced. On the basis of these findings and the phylogeny of GLX in oxygenic phototrophs, we propose that the GLX system scavenges MG produced in chloroplasts during photosynthesis.     

Elevated CO2 alters tissue balance of nitrogen metabolism and downregulates nitrogen assimilation and signalling gene expression in wheat seedlings receiving high nitrate supply

Tissue and canopy-level evidence suggests that elevated carbon dioxide (EC) inhibits shoot nitrate assimilation in plants and thereby affects nitrogen (N) and protein content of the economic produce. It is speculated that species or genotypes relying more on root nitrate assimilation can adapt better under EC due to the improved/steady supply of reductants required for nitrate assimilation. A study was conducted to examine the effect of EC on N assimilation and associated gene expression in wheat seedlings. Wheat genotypes, BT-Schomburgk (BTS) with comparatively high leaf nitrate reductase (NR) activity and Gluyas Early (GE) with high root NR activity were grown in hydroponic culture for 30 days with two different nitrate levels (0.05 mM and 5 mM) in the climate controlled growth chambers maintained at either ambient (400 ± 10 μmol mol⁻¹) or EC (700 ± 10 μmol mol⁻¹) conditions. Exposure to EC downregulated the activity of enzyme NR and glutamate synthase (GOGAT) in leaf tissues, whereas in roots, activities of both the enzymes were upregulated by exposure to EC. In addition, EC downregulated N assimilation and signalling gene expression under high N availability. Root N assimilation was less affected in comparison with shoot N assimilation; thereby, the proportion of root contribution towards total assimilation was higher. The results suggest that EC could alter and re-programme N assimilation and signalling in wheat seedlings. The genotype and tissue-specific effects of EC on N assimilation also warrants the need for identification of suitable genotypes and revision of fertiliser regime for tapping the beneficial effects of EC conditions.

     

Dynamic modelling of limitations on improving leaf CO2 assimilation under fluctuating irradiance

A dynamic model of leaf CO₂ assimilation was developed as an extension of the canonical steady‐state model, by adding the effects of energy‐dependent non‐photochemical quenching (qE), chloroplast movement, photoinhibition, regulation of enzyme activity in the Calvin cycle, metabolite concentrations, and dynamic CO₂ diffusion. The model was calibrated and tested successfully using published measurements of gas exchange and chlorophyll fluorescence on Arabidopsis thaliana ecotype Col‐0 and several photosynthetic mutants and transformants affecting the regulation of Rubisco activity (rca‐2 and rwt43), non‐photochemical quenching (npq4‐1 and npq1‐2), and sucrose synthesis (spsa1). The potential improvements on CO₂ assimilation under fluctuating irradiance that can be achieved by removing the kinetic limitations on the regulation of enzyme activities, electron transport, and stomatal conductance were calculated in silico for different scenarios. The model predicted that the rates of activation of enzymes in the Calvin cycle and stomatal opening were the most limiting (up to 17% improvement) and that effects varied with the frequency of fluctuations. On the other hand, relaxation of qE and chloroplast movement had a strong effect on average low‐irradiance CO₂ assimilation (up to 10% improvement). Strong synergies among processes were found, such that removing all kinetic limitations simultaneously resulted in improvements of up to 32%.     

High non-photochemical quenching of VPZ transgenic potato plants limits CO2 assimilation under high light conditions and reduces tuber yield under fluctuating light

Under natural conditions, photosynthesis has to be adjusted to fluctuating light intensities.Leaves exposed to high light dissipate excess light energy in form of heat at photosystem II(PSII) by a process called non-photochemical quenching(NPQ). Upon fast transition from light to shade, plants lose light energy by a relatively slow relaxation from photoprotection. Combined overexpression of violaxanthin de-epoxidase(VDE), PSII subunit S(PsbS) and zeaxanthin epoxidase(ZEP) in tobacco accelerates ...     

Oxygen requirement of photosynthetic CO2 assimilation

In the absence of electron acceptors and of oxygen a proton gradient was supported across thylakoid membranes of intact spinach chloroplasts by far-red illumination. It was decreased by red light. Inhibition by red light indicates effective control of cyclic electron flow by Photosystem II. Inhibition was released by oxygen which supported a large proton gradient. Oxygen appeared to act as electron acceptor simultaneously preventing over-reduction of electron carriers of the cyclic electron transport pathway. It thus has an important regulatory function in electron transport. Under anaerobic conditions, the inhibition of electron transport caused by red illumination could also be released and a large proton gradient could be established by oxaloacetate, nitrite and 3-phosphoglycerate, but not by bicarbonate. In the absence of oxygen, ATP levels remained low in chloroplasts illuminated with red light even when bicarbonate was present. They increased when electron acceptors were added which could release the over-reduction of the electron transport chain. Inhibition of electron transport in the presence of bicarbonate was relieved and CO2-fixation was initiated by oxygen concentrations as low as about 10 microM. Once CO2 fixation was initiated, very low oxygen levels were sufficient to sustain it. The results support the assumption that pseudocyclic electron transport is necessary to poise the electron transport chain so that a proper balance of linear and cyclic electron transport is established to supply ATP for CO2 reduction.     

Increasing water and nitrogen availability enhanced net ecosystem CO2 assimilation of a temperate semiarid steppe

Boron (B) is an essential micronutrient, whose deficiency is common in boreal forests. Our aim was to investigate the effects of the B supply on the retranslocation of micro- and macro nutrients in seedlings of Betula pendula Roth. One-year-old seedlings were grown under three different levels of B: 0%, 30% and 100% of the standard level for complete nutrient solution. Half of the seedlings were harvested after summer period and another half when leaves abscised. Boron was not resorbed in significant amounts from senescing birch leaves prior to abscission. The only micronutrients resorbed were Zn and Ni. Three macronutrients, N, P, and S, were resorbed efficiently from senescing leaves and accumulated into the stems. The resorption of nutrients was the mostly pronounced in B0 seedlings and minimal in B30 seedlings, which, however, showed the highest accumulation of nutrients during autumn period at least partly independently from the resorption from senescing leaves. Boron was shown to be an immobile element in silver birch seedlings that was not withdrawn from senescing leaves prior to abscission. This may increase the B availability for other tree species but also increase the potential for its leaching.     

Use of heterotrophic CO2 assimilation as a measure of metabolic activity in planktonic and sessile bacteria

We have examined whether assimilation of CO2 can be used as a measure of metabolic activity in planktonic and sessile heterotrophic bacteria. CO2 assimilation by environmental samples and pure cultures of heterotrophic bacteria was studied using 14CO2 and 13CO2 as tracers. Heterotrophic growth on complex organic substrates resulted in assimilation of CO2 into cell biomass by activated sludge, drinking water biofilm, and pure cultures of Escherichia coli ATCC 25922, Es. coli ATCC 13706, Rhodococcus ruber, Burkholderia sp., Bacillus circulans, Pseudomonas putida, Pseudomonas stutzeri, and Pseudomonas aeruginosa. Analysis of 13C-labelled phospholipid fatty acids (PLFAs) confirmed that heterotrophic bacteria may assimilate 13CO2 into cell macromolecules such as membrane lipids. All major PLFAs extracted from activated sludge and drinking water biofilm samples were enriched in 13C after incubation with CO2. Between 1.4% and 6.5% of the biomass produced by cultures of P. putida and a drinking water biofilm during growth in complex media was apparently derived from assimilation of CO2. Resting cells assimilated less CO2 compared to actively growing cells, and CO2 assimilation activity correlated with the amount of biomass produced during heterotrophic growth. The 14CO2 assimilation assay was evaluated as a tool to examine inhibitory effects of biocides on planktonic and sessile heterotrophs (biofilms). On the basis of 14CO2 assimilation activity, the minimum inhibitory concentration (MIC) of benzalkonium chloride was estimated to 21.1 and 127.2 mg l(-1) for planktonic and biofilm samples, respectively. The results indicate that assimilation of isotopically labelled CO2 can be used as a relatively simple measure of metabolic activity in heterotrophic bacteria. CO2 assimilation assays may be used to study the effects of antimicrobial agents on growth and survival of planktonic and sessile heterotrophic organisms.     

Effect of bicarbonates and CO2 concentration increase in tissues on assimilation of ammonium nitrogen in cattle

The feeding of carboxyline and cobalt salts to cattle young fattener receiving the concentrate-silo rations with synthetic nitrogen-containing substances (diammonium phosphate and urea) is accompanied by an increase in the concentration of bicarbonates and CO2 in blood and citric acid in blood plasma with a decrease of the ketonic bodies content in it. The level of carbon dioxide in tissues being increased, the content of ammonium nitrogen in the rumen fluid lowers and the activity of transaminases in blood plasma, the content of glutamate in the liver and that of urea in the rumen fluid increase which evidences for an intensified transformation of the ration nitrogen in the organism. The performance of animals is increased.     

Constraints to nitrogen acquisition of terrestrial plants under elevated CO2

A key part of the uncertainty in terrestrial feedbacks on climate change is related to how and to what extent nitrogen (N) availability constrains the stimulation of terrestrial productivity by elevated CO₂ (eCO₂), and whether or not this constraint will become stronger over time. We explored the ecosystem‐scale relationship between responses of plant productivity and N acquisition to eCO₂ in free‐air CO₂ enrichment (FACE) experiments in grassland, cropland and forest ecosystems and found that: (i) in all three ecosystem types, this relationship was positive, linear and strong (r² = 0.68), but exhibited a negative intercept such that plant N acquisition was decreased by 10% when eCO₂ caused neutral or modest changes in productivity. As the ecosystems were markedly N limited, plants with minimal productivity responses to eCO₂ likely acquired less N than ambient CO₂‐grown counterparts because access was decreased, and not because demand was lower. (ii) Plant N concentration was lower under eCO₂, and this decrease was independent of the presence or magnitude of eCO₂‐induced productivity enhancement, refuting the long‐held hypothesis that this effect results from growth dilution. (iii) Effects of eCO₂ on productivity and N acquisition did not diminish over time, while the typical eCO₂‐induced decrease in plant N concentration did. Our results suggest that, at the decennial timescale covered by FACE studies, N limitation of eCO₂‐induced terrestrial productivity enhancement is associated with negative effects of eCO₂ on plant N acquisition rather than with growth dilution of plant N or processes leading to progressive N limitation.     

CO2 mineralization induced by fungal nitrate assimilation

Formation of CaCO3 induced by fungal physiological activities is a potential way to sequestrate atmospheric CO2 in ecosystem. Alternaria sp. is a saprophytic fungus isolated from a forest soil. We examined the precipitation of CaCO3 induced by the fungus in response to different levels of Ca(NO3)2 or CaCl2 in agar media, and the biogenesis of CaCO3 was verified by low δ13C value. The formed CaCO3 was identified as calcite by X-ray diffraction analysis. Square, rectangular and rhombic CaCO3 crystals and amorphous calcium carbonate were observed around mycelia at higher levels of Ca(NO3)2. Acidification occurred in media at low concentrations (0 and 0.0002 M) of Ca(NO3)2, and no CaCO3 formed in these media. The quantities of CaCO3 formed in media increased with increasing concentrations of Ca(NO3)2 and were significantly correlated to fungal biomass, pH value and nitrite concentrations. No CaCO3 was formed in media with CaCl2 at all levels. These results collectively indicated that the formation of CaCO3 can be induced by the fungal assimilation of nitrate. The study also revealed that biogenic crystal of CaCO3 tended to grow on a silicon nucleus and the amorphous calcium carbonate (ACC) was the transient stage of CaCO3 crystal.     

Acetate and CO2 assimilation by Methanothrix concilii.

Biosynthetic pathways in Methanothrix concilii, a recently isolated aceticlastic methanogen, were studied by 13C-nuclear magnetic resonance spectroscopy. Labeling patterns of amino acids, lipids, and carbohydrates were determined. Similar to other methanogens, acetate was carboxylated to pyruvate, which was further converted to amino acids by various biosynthetic pathways. The origin of carbon atoms in glutamate, proline, and arginine clearly showed that an incomplete tricarboxylic acid cycle operating in the oxidative direction was used for their biosynthesis. Isoleucine was synthesized via citramalate, which is a typical route for methanogens. As with Methanosarcina barkeri, an extensive exchange of the label between the carboxyl group of acetate and CO2 was observed. Lipids predominantly contained diphytanyl chains, the labeling of which indicated that biosynthesis proceeded through mevalonic acid. Labeling of the C-1,6 of glucose from [2-13C]acetate is consistent with a glucogenic route for carbohydrate biosynthesis. Except for the different origins of the methyl group of methionine, the metabolic properties of Methanothrix concilii are closely related to those of Methanosarcina barkeri.     

24-epibrassinolide improves cucumber photosynthesis under hypoxia by increasing CO2 assimilation and photosystem II efficiency

Seedlings of the hypoxia-sensitive cucumber cultivar were hydroponically grown under hypoxia for 7 d in the presence or absence of 24-epibrassinolide (EBR, 2.1 nM). Hypoxia significantly inhibited growth, while EBR partially counteracted this inhibition. Leaf net photosynthetic rate (P _N), stomatal conductance, transpiration rate, and water-use efficiency declined greatly, while the stomatal limitation value increased significantly. The maximum net photosynthetic rate was strongly reduced by hypoxia, indicating that stomatal limitation was not the only cause of the P _N decrease. EBR markedly diminished the harmful effects of hypoxia on P _N as well as on stomata openness. It also greatly stimulated CO₂ fixation by the way of increasing the carboxylation capacity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), ribulose-1,5-bisphosphate regeneration, Rubisco activity, and the protection of Rubisco large subunit from degradation. Our data indicated that photosystem (PS) II was damaged by hypoxia, while EBR had the protective effect. EBR further increased nonphotochemical quenching that could reduce photodamage of the PSII reaction center. The proportion of absorbed light energy allocated for photochemical reaction (P) was reduced, while both nonphotochemical reaction dissipation of light energy and imbalanced partitioning of excitation energy between PSI and PSII increased. EBR increased P and alleviated this imbalance. The results suggest that both stomatal and nonstomatal factors limited the photosynthesis of cucumber seedlings under hypoxia. EBR alleviated the growth inhibition by improving CO₂ asimilation and protecting leaves against PSII damage.     

Regulation of the Calvin cycle for CO2 fixation as an example for general control mechanisms in metabolic cycles.

The theory of a metabolic cycle with the main portion of its intermediates remaining inside the cycle during one turnover has been developed. On this basis, the regulation of the Calvin cycle is analyzed. It is demonstrated that not only the reactions of non-equilibrium enzymes, as the carboxylation of ribulose 1,5-bisphosphate, but reactions that operate close to a thermodynamic equilibrium, especially the reduction of 3-phosphoglycerate and the transketolase reaction can significantly influence the total turnover period in the Calvin cycle. The role of compensating mechanisms in the maintenance of the photosynthesis rate upon changes of environmental conditions and of enzyme contents is analyzed for the Calvin cycle. It is shown that the change of the total quantity of the metabolites is one of the main self-regulated mechanisms in the Calvin cycle. A change of the ATP/ADP ratio can be used by the cell to maintain the CO2 assimilation rate, when the total quantity of the metabolites is changed. The developed analysis permits to explain some experimental data obtained with transgenic plants with restricted efflux of carbon from the chloroplasts.