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PubMed2005

A new arrangement of (beta/alpha)8 barrels in the synthase subunit of PLP synthase.

Pyridoxal 5'-phosphate (PLP, vitamin B6), a cofactor in many enzymatic reactions, has two distinct biosynthetic routes, which do not coexist in any organism. Two proteins, known as PdxS and PdxT, together form a PLP synthase in plants, fungi, archaea, and some eubacteria. PLP synthase is a heteromeric glutamine amidotransferase in which PdxT produces ammonia from glutamine and PdxS combines ammonia with five- and three-carbon phosphosugars to form PLP. In the 2.2-A crystal structure, PdxS is a cylindrical dodecamer of subunits having the classic (beta/alpha)8 barrel fold. PdxS subunits form two hexameric rings with the active sites positioned on the inside. The hexamer and dodecamer forms coexist in solution. A novel phosphate-binding site is suggested by bound sulfate. The sulfate and another bound molecule, methyl pentanediol, were used to model the substrate ribulose 5-phosphate, and to propose catalytic roles for residues in the active site. The distribution of conserved surfaces in the PdxS dodecamer was used to predict a docking site for the glutaminase partner, PdxT.

Ammonia↗
PubMed2003

Methylophaga natronica sp. nov., a new alkaliphilic and moderately halophilic, restricted-facultatively methylotrophic bacterium from soda lake of the Southern Transbaikal region.

A new, moderately haloalkaliphilic and restricted-facultatively methylotrophic bacterium (strain Bur2T) with the ribulose monophosphate pathway of carbon assimilation is described. The isolate, which utilizes methanol, methylamine and fructose, is an aerobic, Gram-negative, asporogenous, motile short rod multiplying by binary fission. It is auxotrophic for vitamin B12, and requires NaHCO3 or NaCl for growth in alkaline medium. Cellular fatty acids profile consists primarily of straight-chain saturated C16:0, unsaturated C16:1 and C18:1 acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. Diphosphatidylglycerol is also present. Optimal growth conditions are 25-29 degrees C, pH 8.5-9.0 and 2-3% (w/v) NaCl. Cells accumulate ectoine and glutamate as the main osmoprotectants. The G + C content of the DNA is 45.0 mol%. Based on 16S rDNA sequence analysis and DNA-DNA relatedness (25-35%) with type strains of marine and soda lake methylobacteria belonging to the genus Methylophaga, the novel isolate was classified as a new species of this genus and named Methylophaga natronica (VKM B-2288T).

Aerobiosis↗
PubMed2000

Is there scope for improving balance between RuBP-regeneration and carboxylation capacities in wheat at elevated CO2?

Carboxylation and RuBP-regeneration capacities, which determine light-saturated photosynthetic rate, were analysed in leaves of spring wheat (Triticum aestivum L. cv. Minaret) grown under different atmospheric CO2 partial pressure (pCa) and N supply regimes. Capacities were estimated from a large number of gas exchange, Rubisco and ATP-synthase content measurements, and from these, the pCa at which the two capacities are equal was derived, to allow direct comparison with growth pCa. Acclimation of the balance between the two capacities to growth at elevated pCa in wheat was only partial and appears to occur mostly in older flag leaves and at low N. However, in contrast to conclusions drawn from previous analyses of these data, there was evidence of a specific effect of growth at 70 Pa pCa, where carboxylation capacity is reduced more than RuBP-regeneration capacity for a given leaf N content. A model was used to estimate the effects of fluctuations in PPFD and temperature in the growth environment on the optimal balance between these capacities. This showed that the observed balance between carboxylation and RuBP-regeneration capacities in young wheat leaves could be consistent with adaptation to the current, or even the preindustrial pCa.

Adenosine Triphosphate↗
PubMed2001

Small decreases in SBPase cause a linear decline in the apparent RuBP regeneration rate, but do not affect Rubisco carboxylation capacity.

The response of net photosynthetic CO(2) uptake (A) to increasing leaf intercellular CO(2) concentration (c(i)) was determined in antisense Nicotiana tabacum plants, derived from six independent transformation lines, displaying a range of sedoheptulose-1, 7-bisphosphatase (SBPase) activities. The maximum in vivo ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) carboxylation (V(c,max)) and RuBP regeneration (J(max)) rates were calculated from the steady-state measurements of the A to c(i) response curves. In plants with reductions in SBPase activity of between 9% and 60%, maximum RuBP regeneration capacity declined linearly (r(2)=0.79) and no significant change in apparent in vivo Rubisco activity (V(c,max)) was observed in these plants. No correlation between V(c,max) and a decrease in capacity for RuBP regeneration was observed (r(2)=0.14) in the SBPase antisense plants. These data demonstrate that small decreases in SBPase activity limit photosynthetic carbon assimilation by reducing the capacity for RuBP regeneration.

Carbon Dioxide↗
PubMed2002

Effects of water deficit and its interaction with CO(2) supply on the biochemistry and physiology of photosynthesis in sunflower.

Photosynthetic responses of sunflower plants grown for 52 d in ambient and elevated CO(2) (A=350 or E=700 micromol mol(-1), respectively) and subjected to no (control), mild or severe water deficits after 45 d were analysed to determine if E modifies responses to water deficiency. Relative water content, leaf water potential (Psi(w)) and osmotic potential decreased with water deficiency, but there were no effects of E. Growth in E decreased stomatal conductance (g(s)) and thereby transpiration, but increased net CO(2) assimilation rate (P(n), short-term measurements); therefore, water-use efficiency increased by 230% (control plants) and 380% (severe stress). Growth in E did not affect the response of P(n) to intercellular CO(2) concentration, despite a reduction of 25% in Rubisco content, because this was compensated by a 32% increase in Rubisco activity. Analysis of chlorophyll a fluorescence showed that changes in energy metabolism associated with E were small, despite the decreased Rubisco content. Water deficits decreased g(s) and P(n): metabolic limitation was greater than stomatal at mild and severe deficit and was not overcome by elevated CO(2). The decrease in P(n) with water deficiency was related to lower Rubisco activity rather than to ATP and RuBP contents. Thus, there were no important interactions between CO(2) during growth and water deficit with respect to photosynthetic metabolism. Elevated CO(2 )will benefit sunflower growing under water deficit by marginally increasing P(n), and by slowing transpiration, which will decrease the rate and severity of water deficits, with limited effects on metabolism.

Adenosine Triphosphate↗
PubMed2004

Seasonal change in the balance between capacities of RuBP carboxylation and RuBP regeneration affects CO2 response of photosynthesis in Polygonum cuspidatum.

The balance between the capacities of RuBP (ribulose-1,5-bisphosphate) carboxylation (V(cmax)) and RuBP regeneration (expressed as the maximum electron transport rate, J(max)) determines the CO(2) dependence of the photosynthetic rate. As it has been suggested that this balance changes depending on the growth temperature, the hypothesis that the seasonal change in air temperature affects the balance and modulates the CO(2) response of photosynthesis was tested. V(cmax) and J(max) were determined in summer and autumn for young and old leaves of Polygonum cuspidatum grown at two CO(2) concentrations (370 and 700 micromol mol(-1)). Elevated CO(2) concentration tended to reduce both V(cmax) and J(max) without changing the J(max):V(cmax) ratio. The seasonal environment, on the other hand, altered the ratio such that the J(max):V(cmax) ratio was higher in autumn leaves than summer leaves. This alternation made the photosynthetic rate more dependent on CO(2) concentration in autumn. Therefore, when photosynthetic rates were compared at growth CO(2) concentration, the stimulation in photosynthetic rate was higher in young-autumn than in young-summer leaves. In old-autumn leaves, the stimulation of photosynthesis brought by a change in the J(max):V(cmax) ratio was partly offset by accelerated leaf senescence under elevated CO(2). Across the two seasons and the two CO(2) concentrations, V(cmax) was strongly correlated with Rubisco and J(max) with cytochrome f content. These results suggest that seasonal change in climate affects the relative amounts of photosynthetic proteins, which in turn affect the CO(2) response of photosynthesis.

Carbon Dioxide↗
PubMed2005

Irradiance and phenotype: comparative eco-development of sun and shade leaves in relation to photosynthetic CO2 diffusion.

The subject of this paper, sun leaves are thicker and show higher photosynthetic rates than the shade leaves, is approached in two ways. The first seeks to answer the question: why are sun leaves thicker than shade leaves? To do this, CO2 diffusion within a leaf is examined first. Because affinity of Rubisco for CO2 is low, the carboxylation of ribulose 1,5-bisphosphate is competitively inhibited by O2, and the oxygenation of ribulose 1,5-bisphosphate leads to energy-consuming photorespiration, it is essential for C3 plants to maintain the CO2 concentration in the chloroplast as high as possible. Since the internal conductance for CO2 diffusion from the intercellular space to the chloroplast stroma is finite and relatively small, C3 leaves should have sufficient mesophyll surfaces occupied by chloroplasts to secure the area for CO2 dissolution and transport. This explains why sun leaves are thicker. The second approach is mechanistic or 'how-oriented'. Mechanisms are discussed as to how sun leaves become thicker than shade leaves, in particular, the long-distance signal transduction from mature leaves to leaf primordia inducing the periclinal division of the palisade tissue cells. To increase the mesophyll surface area, the leaf can either be thicker or have smaller cells. Issues of cell size are discussed to understand plasticity in leaf thickness.

Amaranthus↗
PubMed2005

Temperature acclimation of photosynthesis: mechanisms involved in the changes in temperature dependence of photosynthetic rate.

Growth temperature alters temperature dependence of the photosynthetic rate (temperature acclimation). In many species, the optimal temperature that maximizes the photosynthetic rate increases with increasing growth temperature. In this minireview, mechanisms involved in changes in the photosynthesis-temperature curve are discussed. Based on the biochemical model of photosynthesis, change in the photosynthesis-temperature curve is attributable to four factors: intercellular CO2 concentration, activation energy of the maximum rate of RuBP (ribulose-1,5-bisphosphate) carboxylation (Vc max), activation energy of the rate of RuBP regeneration (Jmax), and the ratio of Jmax to Vc max. In the survey, every species increased the activation energy of Vc max with increasing growth temperature. Other factors changed with growth temperature, but their responses were different among species. Among these factors, activation energy of Vc max may be the most important for the shift of optimal temperature of photosynthesis at ambient CO2 concentrations. Physiological and biochemical causes for the change in these parameters are discussed.

Acclimatization↗
PubMed1989

Codon usage in plant genes.

We have examined codon bias in 207 plant gene sequences collected from Genbank and the literature. When this sample was further divided into 53 monocot and 154 dicot genes, the pattern of relative use of synonymous codons was shown to differ between these taxonomic groups, primarily in the use of G + C in the degenerate third base. Maize and soybean codon bias were examined separately and followed the monocot and dicot codon usage patterns respectively. Codon preference in ribulose 1,5 bisphosphate and chlorophyll a/b binding protein, two of the most abundant proteins in leaves was investigated. These highly expressed are more restricted in their codon usage than plant genes in general.

Amino Acid Sequence↗
PubMed1992

Processing of chimeric introns in dicot plants: evidence for a close cooperation between 5' and 3' splice sites.

Splice sites of vertebrate introns are generally not recognized in plant cells. Several lines of evidences have led to the proposal that the mechanism of 3' splice site selection differs in plants and animals (K. Wiebauer, J.J. Herrero, and W. Filipowicz, Mol. Cell. Biol. 8:2042-2051, 1988). To gain a better insight into the mechanistic differences between plant and animal splicing, we constructed chimeric introns consisting partly of dicotyledonous plant and partly of animal intron sequences. Splicing of these chimeric introns was analyzed in transiently transfected tobacco protoplasts. The results show that there are no principal sequence or structural differences between the 3' splice regions of plants and animals. Furthermore, evidence is provided that cooperation between 5' and 3' splice sites takes place and influences their mutual selection.

Animals↗
PubMed1991

Ribulose bisphosphate-induced, slow conformational changes of spinach ribulose bisphosphate carboxylase cause the two types of inflections in the course of its carboxylase reaction.

The cause of the inflection in the course of the carboxylase reaction and the changes in the functioning form of spinach ribulose bisphosphate carboxylase (RuBisCO) during the reaction were elucidated by relating the activity to the protein conformation of RuBisCO using a fluorescence probe, 2-p-toluidinylnaphthalene sulfonate. The activity of RuBisCO in the linear phase was 50 to 60% of that in the initial burst at 0.5 to 1.0 mM ribulose bisphosphate (RuBP) and 65 to 80% at 2 to 5 mM RuBP. The amount and the progress of the decrease in the activity during the reaction had a close relationship to a change in the protein conformation of RuBisCO. The enzyme, the substrate binding sites of which were masked beforehand with carboxyarabinitol bisphosphate, still showed a change of its protein conformation upon addition of RuBP, suggesting that RuBisCO has two (substrate and regulatory) RuBP-binding sites per RuBisCO promoter. RuBisCO required over 2 mM RuBP for binding on the regulatory sites. Both sites also bound 6-phosphogluconate. When both sites were masked with 6-phosphogluconate beforehand, the course of the subsequent carboxylase reaction was linear with time. From these results, I propose that the inflection in the course of the reaction of spinach RuBisCO is a hysteretic response of the enzyme to RuBP bound to both substrate and regulatory sites.

Animals↗
PubMed2005

Photosynthetic acclimation in rice leaves to free-air CO2 enrichment related to both ribulose-1,5-bisphosphate carboxylation limitation and ribulose-1,5-bisphosphate regeneration limitation.

Net photosynthetic rates (Pns) in leaves were compared between rice plants grown in ambient air control and free-air CO2 enrichment (FACE, about 200 micromol mol(-1) above ambient) treatment rings. When measured at the same CO2 concentration, the Pn of FACE leaves decreased significantly, indicating that photosynthetic acclimation to high CO2 occurs. Although stomatal conductance (Gs) in FACE leaves was markedly decreased, intercellular CO2 concentrations (Ci) were almost the same in FACE and ambient leaves, indicating that the photosynthetic acclimation is not caused by the decreased Gs. Furthermore, carboxylation efficiency and maximal Pn, both light and CO2-saturated Pn, were decreased in FACE leaves, as shown by the Pn-Ci curves. In addition, the soluble protein, Rubisco (ribulose-1,5-bisphosphate caboxylase/oxygenase), and its activase contents as well as the sucrose-phosphate synthase activity decreased significantly, while some soluble sugar, inorganic phosphate, chlorophyll and light-harvesting complex II (LHC II) contents increased in FACE leaves. It appears that the photosynthetic acclimation in rice leaves is related to both ribulose-1,5-bisphosphate (RuBP) carboxylation limitation and RuBP regeneration limitation.

Acclimatization↗
PubMed2006

Contribution of fructose-1,6-bisphosphatase and sedoheptulose-1,7-bisphosphatase to the photosynthetic rate and carbon flow in the Calvin cycle in transgenic plants.

To clarify the contributions of fructose-1,6-bisphosphatase (FBPase) and sedoheptulose-1,7-bisphosphatase (SBPase) separately to the carbon flux in the Calvin cycle, we generated transgenic tobacco plants expressing cyanobacterial FBPase-II in chloroplasts (TpF) or Chlamydomonas SBPase in chloroplasts (TpS). In TpF-11 plants with 2.3-fold higher FBPase activity and in TpS-11 and TpS-10 plants with 1.6- and 4.3-fold higher SBPase activity in chloroplasts compared with the wild-type plants, the amount of final dry matter was approximately 1.3-, 1.5- and 1.5-fold higher, respectively, than that of the wild-type plants. At 1,500 micromol m(-2) s(-1), the photosynthetic activities of TpF-11, TpS-11 and TpS-10 were 1.15-, 1.27- and 1.23-fold higher, respectively, than that of the wild-type plants. The in vivo activation state of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and the level of ribulose-1,5-bisphosphate (RuBP) in TpF-11, TpS-10 and TpS-11 were significantly higher than those in the wild-type plants. However, the transgenic plant TpF-9 which had a 1.7-fold higher level of FBPase activity showed the same phenotype as the wild-type plant, except for the increase of starch content in the source leaves. TpS-11 and TpS-10 plants with 1.6- and 4.3-fold higher SBPase activity, respectively, showed an increase in the photosynthetic CO(2) fixation, growth rate, RuBP contents and Rubisco activation state, while TpS-2 plants with 1.3-fold higher SBPase showed the same phenotype as the wild-type plants. These data indicated that the enhancement of either a >1.7-fold increase of FBPase or a 1.3-fold increase of SBPase in the chloroplasts had a marked positive effect on photosynthesis, that SBPase is the most important factor for the RuBP regeneration in the Calvin cycle and that FBPase contributes to the partitioning of the fixed carbon for RuBP regeneration or starch synthesis.

Animals↗
PubMed2006

Physiological basis of seasonal trend in leaf photosynthesis of five evergreen broad-leaved species in a temperate deciduous forest.

The physiological basis of photosynthesis during winter was investigated in saplings of five evergreen broad-leaved species (Camellia japonica L., Cleyera japonica Thunb., Photinia glabra (Thunb.) Maxim., Castanopsis cuspidata (Thunb.) Schottky and Quercus glauca Thunb.) co-occurring under deciduous canopy trees in a temperate forest. We focused on temperature dependence of photosynthetic rate and capacity as important physiological parameters that determine light-saturated rates of net photosynthesis at low temperatures during winter. Under controlled temperature conditions, maximum rates of ribulose bisphosphate carboxylation and electron transport (Vcmax) and Jmax, respectively) increased exponentially with increasing leaf temperature. The temperature dependence of photosynthetic rate did not differ among species. In the field, photosynthetic capacity, determined as Vcmax and Jmax at a common temperature of 25 degrees C (Vcmax(25) and Jmax(25)), increased until autumn and then decreased in species-specific patterns. Values of Vcmax(25) and Jmax(25) differed among species during winter. There was a positive correlation of Vcmax(25) with area-based nitrogen concentration among leaves during winter in Camellia and Photinia. Interspecific differences in Vcmax(25) were responsible for interspecific differences in light-saturated rates of net photosynthesis during winter.

Algorithms↗
PubMed2000

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.

Animals↗
PubMed1991

Determination of effector molecules in L-arabinose-induced bulge formation and lysis of Escherichia coli IFO 3545.

L-Ribulose 5-phosphate (L-Ru5P) was identified as the primary effector molecule of L-arabinose-induced bulge formation in Escherichia coli IFO 3545 observed in nutrient broth with 5% (w/v) sodium chloride. Hyperinduction of L-arabinose isomerase was due to exogenous sodium chloride and the resulting alteration in the balance of the L-arabinose-metabolizing enzymes resulted in accumulation of L-Ru5P. L-Ru5P induced the lysis of an L-arabinose-negative, L-Ru5P 4-epimerase-less mutant, ara-207, even when directly added to the medium but was not active against the wild-type strain. Some L-arabinose-utilizing (L-arabinose-resistant) revertants of ara-207 were still sensitive to L-Ru5P, indicating the involvement of another mutation in L-Ru5P-sensitivity other than genetic lack of L-Ru5P 4-epimerase. Among the various pentose phosphate esters tested, only L-Ru5P could induce lysis of ara-207. The lytic activity of L-Ru5P was attributed to its effect on bacterial sugar nucleotide metabolism which caused secondary accumulation of uridine 5'-diphosphate galactose (UDPGal), which provoked lysis induction.

Arabinose↗