A decade of photorespiratory nitrogen cycling

The Arabidopsis glutamine synthetase2 mutants (gln2-1 and gln2-2) do not have abnormal phenotypes

The Arabidopsis glutamine synthetase2 mutants grow normally in the air, challenging the paradigm that chloroplastic GLUTAMINE SYNTHETASE2 is the primary enzyme to assimilate photorespiratory NH4+.

Redundancy and metabolic function of the glutamine synthetase gene family in poplar

BACKGROUND

Glutamine synthetase (GS; EC: 6.3.1.2, L-glutamate: ammonia ligase ADP-forming) is a key enzyme in ammonium assimilation and metabolism in higher plants. In poplar, the GS family is organized in 4 groups of duplicated genes, 3 of which code for cytosolic GS isoforms (GS1.1, GS1.2 and GS1.3) and one group that codes for the choroplastic GS isoform (GS2). Our previous work suggested that GS duplicates may have been retained to increase the amount of enzyme in a particular cell type.

RESULTS

The current study was conducted to test this hypothesis by developing a more comprehensive understanding of the molecular and biochemical characteristics of the poplar GS isoenzymes and by determinating their kinetic parameters. To obtain further insights into the function of the poplar GS genes, in situ hybridization and laser capture microdissections were conducted in different tissues, and the precise GS gene spatial expression patterns were determined in specific cell/tissue types of the leaves, stems and roots. The molecular and functional analysis of the poplar GS family and the precise localization of the corresponding mRNA in different cell types strongly suggest that the GS isoforms play non-redundant roles in poplar tree biology. Furthermore, our results support the proposal that a function of the duplicated genes in specific cell/tissue types is to increase the abundance of the enzymes.

CONCLUSION

Taken together, our results reveal that there is no redundancy in the poplar GS family at the whole plant level but it exists in specific cell types where the two duplicated genes are expressed and their gene expression products have similar metabolic roles. Gene redundancy may contribute to the homeostasis of nitrogen metabolism in functions associated with changes in environmental conditions and developmental stages.

Increased β-cyanoalanine nitrilase activity improves cyanide tolerance and assimilation in Arabidopsis

Plants naturally produce cyanide (CN) which is maintained at low levels in their cells by a process of rapid assimilation. However, high concentrations of environmental CN associated with activities such as industrial pollution are toxic to plants. There is thus an interest in increasing the CN detoxification capacity of plants as a potential route to phytoremediation. Here, Arabidopsis seedlings overexpressing the Pseudomonas fluorescens β-cyanoalanine nitrilase pinA were compared with wild-type and a β-cyanoalanine nitrilase knockout line (ΔAtnit4) for growth in the presence of exogenous CN. After incubation with CN, +PfpinA seedlings had increased root length, increased fresh weight, and decreased leaf bleaching compared with wild-type, indicating increased CN tolerance. The increased tolerance was achieved without an increase in β-cyanoalanine synthase activity, the other enzyme in the cyanide assimilation pathway, suggesting that nitrilase activity is the limiting factor for cyanide detoxification. Labeling experiments with [¹³C]KCN demonstrated that the altered CN tolerance could be explained by differences in flux from CN to Asn caused by altered β-cyanoalanine nitrilase activity. Metabolite profiling after CN treatment provided new insight into downstream metabolism, revealing onward metabolism of Asn by the photorespiratory nitrogen cycle and accumulation of aromatic amino acids.

Expression pattern of genes encoding nitrate and ammonium assimilating enzymes in Arabidopsis thaliana exposed to short term NaCl stress

Key steps in nitrate nutrition and assimilation were assessed over two weeks in control and 100mM NaCl-exposed Arabidopsis thaliana (Columbia) plants. The data showed that NaCl stress lowered nitrate contents in both leaves and roots. While NaCl stress decreased ammonium contents in leaves, it increased the contents in roots at the end of treatment. A survey of transcript levels of NIA1 (At1g77760) and NIA2 (At1g37130) and nitrate reductase (NR, EC 1.6.1.6) activity in the leaves and roots suggested a major role of NIA2 rather than NIA1 in the regulation of NR by salt stress. A drop in mRNA levels for GLN2 (At5g35630) and GLN1;2 (At1g66200) by salt was associated with a similar inhibition of glutamine synthetase (GS, EC 6.3.1.2) activity in the leaves. In the roots, NaCl stress was found to enhance mRNA levels of GLN2 and cytosolic-encoding genes (GLN1;1 (At5g37600) and GLN1;2).

Impairment of the photorespiratory pathway accelerates photoinhibition of photosystem II by suppression of repair but not acceleration of damage processes in Arabidopsis

Oxygenation of ribulose-1,5-bisphosphate catalyzed by Rubisco produces glycolate-2-P. The photorespiratory pathway, which consists of photorespiratory carbon and nitrogen cycles, metabolizes glycolate-2-P to the Calvin cycle intermediate glycerate-3-P and is proposed to be important for avoiding photoinhibition of photosystem II (PSII), especially in C3 plants. We show here that mutants of Arabidopsis (Arabidopsis thaliana) with impairment of ferredoxin-dependent glutamate synthase, serine hydroxymethyltransferase, glutamate/malate transporter, and glycerate kinase had accelerated photoinhibition of PSII by suppression of the repair of photodamaged PSII and not acceleration of the photodamage to PSII. We found that suppression of the repair process was attributable to inhibition of the synthesis of the D1 protein at the level of translation. Our results suggest that the photorespiratory pathway helps avoid inhibition of the synthesis of the D1 protein, which is important for the repair of photodamaged PSII upon interruption of the Calvin cycle.

Fluctuations of γ-aminobutyrate, γ-hydroxybutyrate, and related amino acids in Arabidopsis leaves as a function of the light–dark cycle, leaf age, and N stressEditorial decisions for this paper were made by Robert Ireland, Associate Editor, Canadian Journal of Botany

To gain further insight into the metabolic role of γ-aminobutyrate (GABA), we determined the pool sizes of GABA and its catabolic products, alanine and γ-hydroxybutyrate (GHB), as well as key amino acids (Glu, Gln, Asp, Asn, Pro, Gly, Ser), in Arabidopsis leaves as a function of the light–dark cycle, leaf age (old versus young), and N stress (continuous versus interrupted N supply). Regardless of time of day and leaf age, there was a close relationship among Glu, GABA, and GHB when N was supplied continuously, indicating that GABA and GHB were probably derived exclusively from Glu and GABA, respectively. Ala was also closely linked to GABA in young leaves, but not in old leaves, a result consistent with the existence of multiple sources of Ala. The nature of the responses of GABA and GHB to an interrupted N supply depended on leaf age, and differed from responses exhibited by Glu, Gln, and Asn. Overall fluctuations in primary amino acids under both continuous and interrupted N supply, as well as those associated with photorespiration, aging, and stress, suggest that the old and young leaves chosen for study here function in Arabidopsis as source and sink leaves, respectively.

Land plants equilibrate O2 and CO2 concentrations in the atmosphere

The role of land plants in establishing our present day atmosphere is analysed. Before the evolution of land plants, photosynthesis by marine and fresh water organisms was not intensive enough to deplete CO(2) from the atmosphere, the concentration of which was more than the order of magnitude higher than present. With the appearance of land plants, the exudation of organic acids by roots, following respiratory and photorespiratory metabolism, led to phosphate weathering from rocks thus increasing aquatic productivity. Weathering also replaced silicates by carbonates, thus decreasing the atmospheric CO(2) concentration. As a result of both intensive photosynthesis and weathering, CO(2 )was depleted from the atmosphere down to low values approaching the compensation point of land plants. During the same time period, the atmospheric O(2) concentration increased to maximum levels about 300 million years ago (Permo-Carboniferous boundary), establishing an O(2)/CO(2) ratio above 1000. At this point, land plant productivity and weathering strongly decreased, exerting negative feedback on aquatic productivity. Increased CO(2) concentrations were triggered by asteroid impacts and volcanic activity and in the Mesozoic era could be related to the gymnosperm flora with lower metabolic and weathering rates. A high O(2)/CO(2) ratio is metabolically linked to the formation of citrate and oxalate, the main factors causing weathering, and to the production of reactive oxygen species, which triggered mutations and stimulated the evolution of land plants. The development of angiosperms resulted in a decrease in CO(2) concentration during the Cenozoic era, which finally led to the glacial-interglacial oscillations in the Pleistocene epoch. Photorespiration, the rate of which is directly related to the O(2)/CO(2) ratio, due to the dual function of Rubisco, may be an important mechanism in maintaining the limits of O(2) and CO(2) concentrations by restricting land plant productivity and weathering.

Correlation of ASN2 gene expression with ammonium metabolism in Arabidopsis

In Arabidopsis, asparagine (Asn) synthetase is encoded by a small gene family (ASN1, ASN2, and ASN3). It has been shown that ASN1 and ASN2 exhibit reciprocal gene expression patterns toward light and metabolites. Moreover, changes in total free Asn levels parallel the expression of ASN1, but not ASN2. In this study, we show that ASN2 expression correlates with ammonium metabolism. We demonstrate that the light induction of ASN2 is ammonium dependent. The addition and removal of ammonium exerted fast and reciprocal effects on the levels of ASN2 mRNA, specifically under light-grown conditions. NaCl and cold stress increased cellular free ammonium and ASN2 mRNA levels in a coordinated manner, suggesting that the effects of stress on ASN2 expression may be mediated via accumulation of ammonium. The correlation between ASN2 and cellular ammonium metabolism was further demonstrated by analysis of ASN2 transgenic plants. When plants were grown on Murashige and Skoog medium containing 50 mm ammonium, ASN2 overexpressors accumulated less endogenous ammonium compared with the wild-type Colombia-0 and ASN2 underexpressors. When plants were subjected to high-light irradiance, ammonium levels built up. Under such conditions, ASN2 underexpressors accumulated more endogenous ammonium than the wild-type Colombia-0 and ASN2 overexpressors. These results support the notion that ASN2 is closely correlated to ammonium metabolism in higher plants.

Subcellular NH4 + flux analysis in leaf segments of wheat (Triticum aestivum)

•  We report the first use of tracer ¹³ NH₄ ⁺ (¹³ N-ammonium) efflux and retention data to analyse subcellular fluxes and compartmentation of NH₄ ⁺ in the leaves of a higher plant (wheat, Triticum aestivum). •  Leaf segments, 1-2 mm, were obtained from 8-d-old seedlings. The viability of the segments, and stability of NH ₄ ⁺ acquisition over time, were confirmed using oxygen-exchange and NH ₄ ⁺ -depletion measurements. Fluxes of NH ₄ ⁺ and compartment sizes were estimated using tracer efflux kinetics and retention data. •  Influx and efflux across the plasma membrane, half-lives of exchange and cytosolic pool sizes were broadly similar to those in root systems. As the external concentration of NH ₄ ⁺ ([NH ₄ ⁺ ] _o ) increased from 10 µ m to 10 m m , both influx and efflux greatly increased, with a sixfold increase in the ratio of efflux to influx. Half-lives were similar among treatments, except at [NH ₄ ⁺ ] _o  = 10 m m , where they declined. Concentrations of NH ₄ ⁺ in the cytosol ([NH ₄ ⁺ ] _c ) increased from 2.6 to 400 m m . •  Although [NH ₄ ⁺ ] _c became large as [NH ₄ ⁺ ] _o increased, the ratio of [NH ₄ ⁺ ] _c to [NH ₄ ⁺ ] _o decreased more than sixfold. The apparently futile cycling of NH ₄ ⁺ at high [NH ₄ ⁺ ] _o suggested by the large fluxes of NH ₄ ⁺ in both directions across the membrane indicate that leaf cells respond to potentially toxic NH ₄ ⁺ concentrations in a manner similar to root cells.

Isolation of photorespiratory mutants from Lotus japonicus deficient in glutamine synthetase

A mutagenesis programme using ethyl methanesulphonate (EMS) was carried out on Lotus japonicus (Regel) Larsen cv. Gifu in order to isolate photorespiratory mutants in this model legume. These mutants were able to grow in a CO2-enriched atmosphere [0.7% (v/v) CO2] but showed stress symptoms when transferred to air. Among them, three mutants displayed low levels of glutamine synthetase (GS; EC 6.3.1.2) activity in leaves. The mutants accumulated ammonium in leaves upon transfer from 0.7% (v/v) CO2 to air. F1 plants of back crosses to wild type were viable in air and F2 populations segregated 3 : 1 (viable in air : air-sensitive) indicative of a single Mendelian recessive trait. Complementation tests showed that the three mutants obtained were allelic. Chromatography on DEAE-Sephacel used to separate the cytosolic and plastidic GS isoenzymes together with immunological data showed that: (1) mutants were specifically affected in the plastidic GS isoform, and (2) in L. japonicus the plastidic GS isoform eluted at lower ionic strength than the cytosolic isoform, contrary to what happens in most plants. The plastidic GS isoform present in roots of wild type L. japonicus was also absent in roots of the mutants, indicating that this plastidic isoform from roots was encoded by the same gene than the GS isoform expressed in leaf tissue. Viability of mutant plants in high-CO2 conditions indicates that plastidic GS is not essentially required for primary ammonium assimilation. Nevertheless, mutant plants did not grow as well as wild type plants in high-CO2 conditions.

Photorespiration: metabolic pathways and their role in stress protection

Photorespiration results from the oxygenase reaction catalysed by ribulose-1,5-bisphosphate carboxylase/oxygenase. In this reaction glycollate-2-phosphate is produced and subsequently metabolized in the photorespiratory pathway to form the Calvin cycle intermediate glycerate-3-phosphate. During this metabolic process, CO2 and NH3 are produced and ATP and reducing equivalents are consumed, thus making photorespiration a wasteful process. However, precisely because of this inefficiency, photorespiration could serve as an energy sink preventing the overreduction of the photosynthetic electron transport chain and photoinhibition, especially under stress conditions that lead to reduced rates of photosynthetic CO2 assimilation. Furthermore, photorespiration provides metabolites for other metabolic processes, e.g. glycine for the synthesis of glutathione, which is also involved in stress protection. In this review we describe the use of photorespiratory mutants to study the control and regulation of photorespiratory pathways. In addition, we discuss the possible role of photorespiration under stress conditions, such as drought, high salt concentrations and high light intensities encountered by alpine plants.

THE MOLECULAR-GENETICS OF NITROGEN ASSIMILATION INTO AMINO ACIDS IN HIGHER PLANTS

Nitrogen assimilation is a vital process controlling plant growth and development. Inorganic nitrogen is assimilated into the amino acids glutamine, glutamate, asparagine, and aspartate, which serve as important nitrogen carriers in plants. The enzymes glutamine synthetase (GS), glutamate synthase (GOGAT), glutamate dehydrogenase (GDH), aspartate aminotransferase (AspAT), and asparagine synthetase (AS) are responsible for the biosynthesis of these nitrogen-carrying amino acids. Biochemical studies have revealed the existence of multiple isoenzymes for each of these enzymes. Recent molecular analyses demonstrate that each enzyme is encoded by a gene family wherein individual members encode distinct isoenzymes that are differentially regulated by environmental stimuli, metabolic control, developmental control, and tissue/cell-type specificity. We review the recent progress in using molecular-genetic approaches to delineate the regulatory mechanisms controlling nitrogen assimilation into amino acids and to define the physiological role of each isoenzyme involved in this metabolic pathway.

Glycine decarboxylase complex from higher plants. Molecular cloning, tissue distribution and mass spectrometry analyses of the T protein

cDNA clones encoding the precursor of the T protein of the glycine decarboxylase complex have been isolated from a pea leaf cDNA library in lambda gt11. The longest cDNA insert of 1430 bp encodes a polypeptide of 408 amino acid residues of which 30 residues constitute an N-terminal cleavable presequence and 378 residues make up the mature protein. Several results confirmed the identity of the cDNA and the exactness of the predicted primary structure. Firstly, we purified the T protein to homogeneity and its mass was measured by mass spectrometry. The mass obtained (40966 +/- 5 Da) was the value predicted from the cDNA (40961 Da). Secondly, the purified T protein was chemically cleaved with cyanogen bromide and the peptide fragments were analysed by high-performance liquid chromatography/electrospray ionization mass spectrometry and/or fast-atom-bombardment mass spectrometry. The mass values of all the peptides generated by chemical cleavage and measured by these techniques were very close to the values calculated from the predicted primary structure. Thirdly, microsequencing of some of these peptides, which represent 35% of the total protein, fits perfectly with the primary structure deduced from the cDNA. In the present HPLC/electrospray ionization MS studies we never detected the presence of covalently bound tetrahydropteroylpolyglutamate (H4PteGlun), either in the native T protein or in the different peptide fragments generated by the chemical cleavage. The absence of H4PteGlun bound to the T protein in our experimental conditions demonstrates that H4PteGlun is not covalently linked to the T protein. Northern blot analysis showed that the steady-state level of the mRNA corresponding to the T protein was high in green leaves compared to the level in etiolated leaves (approximately 8-10-fold higher). Surprisingly, a non-negligible amount of mRNA corresponding to the T protein was present in roots whereas the mRNA encoding the H protein was not detectable. Western blot analysis showed that the P, L and T proteins of the glycine decarboxylase complex were present in roots whereas the H protein was not detectable. Southern hybridization to pea genomic DNA indicated the presence of a single gene encoding the T protein of the glycine decarboxylase complex in the haploid genome.

Two classes of differentially regulated glutamine synthetase genes are expressed in the soybean nodule: a nodule-specific class and a constitutively expressed class

We have characterized two sets of cDNA clones representing the glutamine synthetase (GS) mRNA in soybean nodules. Using the 3'-untranslated regions of a representative member of each set, as gene member(s) specific probes, we have shown that one set of the GS genes are expressed in a nodule-specific manner, while the other set is expressed in other tissues, besides the nodules. The nodule-specific GS genes are expressed in a developmentally regulated manner in the nodules, independent of the onset of nitrogen fixation. The other class of GS genes is expressed constitutively in all tissues tested, but its expression level is dramatically enhanced in nodules following onset of N2 fixation. The latter set of genes is also expressed in cotyledons of germinating seedlings in a developmentally regulated manner. Analysis of hybrid select translation products and genomic Southern blots suggests that multiple gene members in each class are expressed in the nodules.

A promoter sequence involved in cell-specific expression of the pea glutamine synthetase GS3A gene in organs of transgenic tobacco and alfalfa

The DNA sequence of the pea cytosolic glutamine synthetase GS3A gene promoter has been determined and the start of transcription mapped using S1 nuclease. The full-length promoter and a series of 5' deletions were fused to beta-glucuronidase (GUS) and introduced into transgenic tobacco and alfalfa. In transgenic tobacco the GS3A promoter directed GUS expression in the phloem cells of the vasculature in leaves, stems and roots. GUS expression was also detected in the vasculature of cotyledons and the root tips of germinating T1 seedlings. The promoter conferred a similar expression pattern in transgenic alfalfa, and expression was also observed in root nodules. Nodule expression was located in nodule primordia, as well as the meristem, symbiotic zone, and vasculature of mature nodules. The promoter was found to be active even when deleted to -132 relative to the start of transcription. DNA mobility-shift analysis identified a protein present in nuclear and whole-cell plant extracts which bound to a 17 bp DNA element contained within the minimal -132 promoter required for expression.

Pea leaf mitochondrial pyruvate dehydrogenase complex is inactivated in vivo in a light-dependent manner

We examined the effect of light on the activity of the mitochondrial pyruvate dehydrogenase complex (mt-PDC) by using intact green pea (Pisum sativum) seedlings. Upon illumination there is an initial drop in mtPDC activity followed by oscillations that dampen during the initial period of photosynthesis to a steady-state level of one-fourth or less of the mtPDC activity measured in the dark. The initial light-dependent decrease in mtPDC activity is inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea (an inhibitor of photosystem II of photosynthesis) and does not occur in etiolated seedlings. Therefore, the effect of light is indirect and most likely associated with photosynthesis and/or photorespiration. Conditions that would be unfavorable for photorespiration also inhibited the light-dependent decrease in mtPDC activity.