The Interaction of Metal Ions with Ribulose 1,5-Diphosphate Carboxylase from Spinach

In silico Identification of Ergosterol as a Novel Fungal Metabolite Enhancing RuBisCO Activity in Lycopersicum esculentum

RuBisCO (EC 4.1.1.39), a key enzyme found in stroma of chloroplast, is important for fixing atmospheric CO2 in plants. Alterations in the activity of RuBisCO could influence photosynthetic yield. Therefore, to understand the activity of the protein, knowledge about its structure is pertinent. Though the structure of Nicotiana RuBisCO has been modeled, the structure of tomato RuBisCO is still unknown. RuBisCO extracted from chloroplasts of tomato leaves was subjected to MALDI-TOF-TOF followed by Mascot Search. The protein sequence based on gene identification numbers was subjected to in silico model construction, characterization and docking studies. The primary structure analysis revealed that protein was stable, neutral, hydrophilic and has an acidic pI. The result though indicates a 90 % homology with other members of Solanaceae but differs from the structure of Arabidopsis RuBisCO. Different ligands were docked to assess the activity of RuBisCO against these metabolite components. Out of the number of modulators tested, ergosterol had the maximum affinity (E = -248.08) with RuBisCO. Ergosterol is a major cell wall component of fungi and has not been reported to be naturally found in plants. It is a known immune elicitor in plants. The current study throws light on its role in affecting RuBisCO activity in plants, thereby bringing changes in the photosynthetic rate.

Discoveries in Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase): a historical perspective

Historic discoveries and key observations related to Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase), from 1947 to 2006, are presented. Currently, around 200 papers describing Rubisco research are published each year and the literature contains more than 5000 manuscripts on the subject. While trying to ensure that all the major events over this period are recorded, this analysis will inevitably be incomplete and will reflect the areas of particular interest to the authors.

Calcium Supports Loop Closure but not Catalysis in Rubisco

Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses CO(2) assimilation in biology. A prerequisite for catalysis is an activation process, whereby an active site lysine is selectively carbamylated. The carbamyl group is then stablised by a metal ion, which in vivo is Mg(2+). Other divalent metal ions can replace Mg(2+) as activators in vitro, but the nature of the metal ion strongly influences the catalytic activity of the enzyme and has a differential effect on the ratio of the carboxylation reaction and the competing oxygenation reaction. Biochemical studies show that calcium promotes carbamylation but not catalysis. To investigate the role of the metal in catalysis, we have determined two structures of the enzyme complexed with Ca(2+) and the transition state analogue 2-carboxy-D-arbinitol-1,5-bisphosphate (2CABP). One of the complexes was prepared by soaking 2CABP into crystals of the enzyme-Ca(2+)-product complex, while the other was obtained by cocrystallising the enzyme with calcium and 2CABP under activating conditions. The two crystals belong to different space groups, and one was merohedrally twinned. Both complexes show very similar three-dimensional features. The enzyme is carbamylated at Lys201, and requisite loops close over the bound ligands in the active site, shielding them from the solvent in a manner similar to the corresponding complex with Mg(2+). However, there are subtle differences that could explain the particular role of Ca(2+) in these processes. The larger radius of the calcium ion and its reduced Lewis-acid character causes a significant increase in the required proton hop distance between the C3 proton and the carbamate on Lys201 in the calcium complex. This alone could explain the inability of calcium to sustain catalysis in Rubisco. Similar effects are also expected on subsequent proton transfer steps in the catalytic cycle. Here we also discuss the effect of metal substitution on the dynamics of the ligands around the metal ion.

Preparation of iron-deficient tissue culture medium by deferoxamine-sepharose treatment and application to the differential actions of apotransferrin and diferric transferrin

We have shown that triiodothyronine-dependent GH1 rat pituitary cell growth in serum-free defined culture required apotransferrin (apoTf) (D. A. Sirbasku, et al., Biochemistry 30, 295-304, 7466-7477, 1991). These studies were done in "low-Fe" medium without Fe(III)/Fe(II) salts. Nonetheless, significant concentrations of iron may have been contributed by other components, making this medium unsuitable for study of the differential effects of apoTf and diferric transferrin (2Fe.Tf). Measuring residual iron in culture medium has been troublesome because the most sensitive method (i.e., atomic absorption) detected levels only in excess of 10 ng/ml and did not distinguish between the forms of iron present. To estimate the Fe(III) available to bind to apoTf, we developed a more sensitive and specific method. Urea-polyacrylamide gel electrophoresis (PAGE) separates apoTf, the two monoferric transferrins, and 2Fe.Tf. [125I]apoTf was incubated with medium, or components, and the formation of [125I]-2Fe.Tf was monitored by urea-PAGE/autoradiography. By this method, the concentration of Fe(III) in low-Fe medium was estimated at 8.4 to 20 ng/ml and the sources were identified. We next sought to remove the Fe(III). Standard chelators were ineffective or cytotoxic. In contrast, an affinity method with deferoxamine-Sepharose depleted greater than or equal to 90% of the Fe(III). In this medium, apoTf and 2Fe.Tf showed differential effects with GH1 cells and with MCF-7, MTW9/PL2, an MDCK cells. With the methods described here, the effects of apoTf and 2Fe.Tf on growth can be studied separately.

Modulation of the tight binding of carboxyarabinitol 1,5-bisphosphate to the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase

The large subunit (L) of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) from Synechococcus PCC 6301 was expressed in Escherichia coli, purified as the octamer L8, and analyzed for its ability to tightly bind the transition state analog, 2-carboxyarabinitol 1,5-bisphosphate (CABP). [14C]CABP remained tightly bound to L8 after challenging with [12C]CABP and gel filtration, indicating that L8 alone without the small subunit (S) could tightly bind CABP. Binding of CABP to L8 induced a shift in the gel filtration profile due to apparent aggregation of L8. Aggregation did not occur with the L8S8-CABP complex nor with L8-CABP in the presence of 150 mM MgCl2. If ionic strength was increased with either KCl or MgCl2 during or after the binding of [14C]CABP to L8, [14C]CABP in the complex exchanged with [12C]CABP and was lost from the protein. Ionic strength strongly affected the rate constant (k4) for [14C]CABP dissociation from the L8-[14C]CABP complex, but had little effect on k4 for the L8S8-CABP complex. The differences in CABP binding characteristics between the L8-CABP and L8S8-CABP complexes demonstrate that S is intimately involved in maintaining the stability of the tight binding of CABP to the active site. These are the same interactions stabilizing the intermediate, 3-keto-2-carboxyarabinitol 1,5-bisphosphate, to native rubisco during CO2 fixation.

D-ribulose-1,5-bisphosphate carboxylase/oxygenase: function-dependent structural changes

The key carboxylating enzyme of the reductive pentose phosphate cycle, D-ribulose-1,5-bisphosphate carboxylase/oxygenase [RuBisCO] isolated from the chemolithoautotrophic, H2-oxidizing bacterium Alcaligenes eutrophus H16 has been analyzed by several different techniques that allow conclusions about structure and function-dependent structural changes. The techniques include a novel approach in which the enzyme was induced to form 2D-crystals suitable for electron microscopy in each of its three stable functional states: as active enzyme [Ea] (in the presence of Mg2+ and HCO3-); as inactivated enzyme [Eia] (in the absence of Mg2+ and HCO3-) and as enzyme locked in an in vitro transition state [CABP-E] (Ea fully saturated with the transition state analogue 2-carboxy-D-arabinitol-1,5-bisphosphate [CABP-E]). In conjunction with X-ray crystallography, X-ray small angle scattering and other biophysical and biochemical data, the results obtained by electron microscopy support the idea that drastic configurational changes occur. Upon transition from Ea to the CABP-E the upper and lower L4S4 halves of the molecule consisting of eight large and eight small subunits (L8S8; MW = 536,000 Da) are assumed to be laterally shifted by as much as 3.6 nm relative to one another while the location of the small subunits on top of the large subunits, and relative to them, remains the same. For the Eia a similar sliding-layer configurational change in the range of 2-2.5 nm is proposed and in addition it is suggested that other configurational/conformational changes take place. The proposed structural changes are discussed with respect to the current model for the tobacco enzyme and correlated with data obtained for various other plant and (cyano) bacterial L8S8 RuBisCOs leading to speculations about structure-function relationships.

The sites for catalysis and activation of ribulosebisphosphate carboxylase share a common domain

The complexation of ribulosebiphosphate carboxylase with CO2, Mg2+, and carboxyarabinitol bisphosphate (CABP) to produce the quaternary enzyme-carbamate-Mg2+-CABP complex closely mimics the formation of the catalytically competent enzyme-carbamate-Mg2+-3-keto-CABP form during enzymatic catalysis. Quaternary complexes were prepared with various metals (Mg2+, Cd2+, Mn2+, Co2+, and Ni2+) and with specifically 13C-enriched ligands. 31P and 13C NMR studies of these complexes demonstrate that the activator CO2 site (carbamate site), the metal binding site, and the substrate binding site are contiguous. It follows that both the carboxylase and oxygenase activities of this bifunctional enzyme are influenced by the structures of the catalytic and activation sites.

Metabolite levels in the stroma of spinach chloroplasts exposed to osmotic stress: Effects of the pH of the medium and exogenous dihydroxyacetone phosphate

The levels of stromal photosynthetic intermediates were measured in isolated intact spinach (Spinacia oleracea L.) chloroplasts exposed to reduced osmotic potentials. Stressed chloroplasts showed slower rates of metabolite accumulation upon illumination than controls. Relative to other metabolites sedoheptulose-1,7-bisphosphate (SBP) and fructose-1,6-bisphosphate (FBP) accumulated in the stroma in the stressed treatments. Under these conditions 3-phosphoglycerate (3-PGA) efflux to the medium was restricted. Chloroplasts previously incubated with [(32)P]KH2PO4 and [(32)P]dihydroxyacetone phosphate ([(32)P]DAP) in the dark were characterized by very high FBP and SBP levels prior to illumination. Metabolism of these pools upon illumination increased with increasing pH of the medium but was consistently inhibited in osmotically stressed chloroplasts. The responses of stromal FBP and SBP pools under hypertonic conditions are discussed in terms of both inhibited light activation of fructose-1,6-bisphosphatase (EC 3.1.3.11) and sedoheptulose-1,7-bisphosphatase (EC 3.1.3.37), and likely increases in stromal ribulose-1,5-bisphosphate carboxylase (EC 4.1.1.39) active-site concentrations.

Modification of carboxyl groups at the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase

Ribulose-1,5-bisphosphate carboxylase/oxygenase from spinach was inactivated by a carboxyl-directed reagent, Woodward's reagent K ( WRK ). The inactivation followed pseudo-first-order kinetics. The reaction order with respect to inactivation by WRK was 1.1, suggesting that inactivation was the consequence of modifying a single residue per active site. The substrate ribulose 1,5-bisphosphate (RBP), two competitive inhibitors, fructose 1,6-bisphosphate (FBP) and sedoheptulose 1,7-bisphosphate (SBP), and a number of sugars-phosphate protected against inactivation by WRK . SBP was a strong protector, displaying a dissociation constant (Kd) of 3 microM with native RBP carboxylase. Pretreatment of RBP carboxylase with diethyl pyrocarbonate prevented WRK incorporation into the enzyme. The enol ester derivative produced by reaction of WRK with RBP carboxylase has a maximal absorbance at 346 nm, and the extinction coefficient was found to be 12300 +/- 700 M-1 cm-1. Spectrophotometric titration of the number of carboxyl groups modified by WRK in RBP carboxylase/oxygenase in the presence and in the absence of SBP suggests that inactivation was associated with the modification of one carboxyl group per active site.

Species variation in kinetic properties of ribulose 1,5-bisphosphate carboxylase/oxygenase

Several kinetic parameters of ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase from different species were measured and compared. The CO2/O2 specificity (VcKo/VoKc) was found to be about 80 in the enzymes from several C3 species and two C4 species. Specificity values of 58 and 70, respectively, were found in enzymes from the C4 plants Setaria italica and Sorghum bicolor. Two enzymes from cyanobacteria had values of about 50. Substitution of Mn2+ for Mg2+ reduced the CO2/O2 specificity by a factor of about 20 for all enzymes except that of Rhodospirillum rubrum, which was reduced by a factor of 10. Values for KMg2+(apparent) measured at 102 microM CO2 were found to vary by a factor of 8 between different RuBP carboxylase/oxygenase enzymes. Enzymes with high KMg2+(apparent) values generally had high Michaelis constants for CO2. The rate of CO2/Mg2+ activation was inhibited by RuBP in all enzymes, although the concentration of RuBP required to inhibit activation in the enzyme from the cyanobacterium Aphanizomenon flos-aquae was increased by an order of magnitude compared to other higher plant structural-type enzymes. The wide variation found in the kinetic properties of RuBP carboxylase/oxygenase isolated from diverse species appears to be determined in part by past evolutionary pressures and the present physicochemical environment in which the enzyme functions.

Interaction of ribulose bisphosphate carboxylase/oxygenase with 2-carboxyhexitol 1,6-bisphosphates

2-C-Carboxy-D-glucitol 1,6-bisphosphate (CGBP) and 2-C-carboxy-D-mannitol 1,6-bisphosphate (CMBP) have been synthesized, isolated, and the structures of these compounds and the derived lactones elucidated by NMR spectroscopy and periodate oxidation. Both carboxyhexitol bisphosphates, which are homologs of the transition state analog 2-C-carboxy-D-arabinitol 1,5-bisphosphate, exhibit competitive inhibiton of ribulose bisphosphate carboxylase/oxygenase (EC 4.1.1.9) isolated from spinach (Spinacia oleracea), with respect to ribulose 1,5-bisphosphate. CMBP was a more potent inhibitor (100-fold) displaying an inhibition constant (Ki at pH 8.0 and 30 degrees C) of 1-2 microM with enzymes from spinach, barley (Hordeum vulgare), and Chromatium vinosum. In contrast the Rhodospirillum rubrum enzyme was inhibited about 40-fold more weakly (Ki = 53 microM at pH 8.0 and 30 degrees C). Both CGBP and CMBP potentiated activation of RuBP carboxylase from spinach and R. rubrum.

Pyrenoid protein from the brown alga Pilayella littoralis

Characterization by peptide mapping and amino acid analysis of the two major pyrenoid polypeptides from the brown alga Pilayella littoralis shows that they are very similar to the subunits of ribulose-1,5-bisphosphate carboxylase (EC 4.1.1.39) from this alga. The observed similarities are discussed in relation to previous pyrenoid protein characterization from members of the Chlorophyceae.

The oxygen-dependent deactivation and reactivation of spinach ribulose-1,5-bisphosphate carboxylase

Ribulose-1,5-bisphosphate carboxylase-oxygenase (3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39) is deactivated by the removal of oxygen, and reversibly reactivated by its readdition to the enzyme solution. A short pulse of oxygen to the anaerobic enzyme solution is sufficient to trigger the reactivation process; the Ka value for this reaction was estimated as 0.12 mM oxygen. The enzyme could not be reactivated under anaerobic conditions by an organic oxidant (benzoylperoxide) or by sulfhydryl group reducing reagents (dithiothreitol or beta-mercaptoethanol), suggesting that the process of reactivation was oxygen specific. Furthermore, the inhibition of the reactivation by superoxide anion scavengers such as Tiron (1,2-dihydroxybenzene-3,5-disulfonic acid), copper penicillamine, hydroxylamine, nitroblue tetrazolium, and ascorbate, indicated that the monovalent reduced oxygen was involved as the reacting species in this process. The deactivation of the enzyme associated with the removal of oxygen was also sensitive to the presence of scavengers of O2(-), suggesting that superoxide anion was also involved in the deactivation process. Both the carboxylase and the oxygenase activities were similarly affected under all the experimental conditions studied. On the basis of these results it is argued that the enzyme molecules are able to reduce oxygen and that superoxide anion causes the deactivation or reactivation of the enzyme.

Nitrogen redistribution during grain growth in wheat (Triticum aestivum L.) : II. Chloroplast senescence and the degradation of ribulose-1,5-bisphosphate carboxylase

The flag leaf of wheat was examined for changes in quantity and activity of ribulose-bisphosphate carboxylase (RuBPCase; EC 4.1.1.39), in the proteolytic degradation of RuBPCase and other native proteins, and in the ultrastructure of the leaf cells during grain development. Proteolytic degradation of RuBPCase at pH 4.8 increased until 8-10 d after anthesis, then declined, and increased again 16-18 d after anthesis. The second peak coincided with the onset of a preferential loss of immunologically recognizable RuBPCase. The specific activity and number of active sites per molecule of RuBPCase did not change during senescence. Examination of ultrastructure with the electron microscope showed little change in the appearance of the mitochondria as the flag leaf aged. Prominent cristae were still evident 35 d after anthesis. In contrast, the chloroplasts showed a progressive disruption of the thylakoid structure and an increasing number of osmiophilic glubules. The double membrane envelope surrounding the chloroplast appeared intact until at least 20 d after anthesis. The tonoplast also appeared intact up to 20 d. At later stages of senescence of the leaf the outer membrane of the chloroplast adjacent to the tonoplast appeared to break but the inner membrane of the envelope appeared intact until at least 35 d after anthesis.

Characterization of the ribulosebisphosphate carboxylase-carbon dioxide-divalent cation-carboxypentitol bisphosphate complex

Ribulosebisphosphate carboxylase forms a stable quaternary complex with CO2, divalent cation, and carboxypentitol bisphosphate. Incorporation of nonexchangeable CO2 into the complex requires the presence of a divalent cation. MG2+, Mn2+, or Co2+ supports stoichiometric binding of CO2 activator. When the quaternary complex is formed in the presence of saturating CO2, stoichiometric amounts of cation are bound in a nonexchangeable fashion. Incorporation of Mn2+ into an enzyme-CO2-Mn2+-carboxypentitol bisphosphate complex permitted investigation of cation environment by electron spin resonance (ESR) techniques. Measurements at 9 and 35 GHz suggest rhombic distortion of the coordination sphere of bound Mn2+. A complex inner sphere liganding of the cation bound in the quaternary complex would account for both the ESR spectra and the marked stability of the complex with respect to cation exchange.

Differential effects of metal ions on Rhodospirillum rubrum ribulosebisphosphate carboxylase/oxygenase and stoichiometric incorporation of HCO3- into a cobalt(III)--enzyme complex

Mg2+ or Mn2+ ions supported both the carboxylase and oxygenase activities of the Rhodospirillum rubrum ribulosebisphosphate carboxylase/oxygenase. For the carboxylase reaction, Mn2+ supported 25% of the maximum activity obtained with Mg2+; oxygenase activity, however, was twice as great with Mn2+ as compared to that with Mg2+. A further differential effect was obtained with Co2+. Co2+ did not support carboxylase activity and, in fact, was a strong inhibitor of Mg2+-dependent carboxylase activity, with a Ki of 10 microM. Co2+ did, however, support oxygenase activity, eliciting about 40% of the Mg2+-dependent oxygenase activity. No other divalent cations supported either activity. With high concentrations of Mg2+ or Mn2+, maximum carboxylase activity was seen after a 5-min activation period; activity decreased to about half of maximum after 30-min activation. A similar time dependence of activation was observed with Mn2+-dependent oxygenase activity but was not seen for Mg2+- or Co2+-dependent activity. Both carboxylase and oxygenase activities were inactivated by the oxidation of Co2+ to Co(III) with the resultant formation of a stable Co(III)--enzyme complex. In the presence of HCO3- (CO2), Co(III) modification was stoichiometric, with two cobalt atoms bound per enzyme dimer. Carbon dioxide was also incorporated into this Co(III)--enzyme complex, but only one molecule per enzyme dimer was bound, indicative of half-the-sites activity. These results thus indicate that there are substantial differences in the metal ion sites of the carboxylase and oxygenase activities of R, rubrum ribulosebisphosphate carboxylase/oxygenase.

Crystalline Ribulose 1,5-Bisphosphate Carboxylase-Oxygenase from Spinach

Spinach fraction I protein (ribulose 1,5-bisphosphate carboxylase-oxy genase, E.C. 4.1.1.39) was crystallized on both an analytical and a preparative scale by vapor diffusion with polyethylene glycol (molecular weight, 6000) used as the precipitant. The identity of the crystalline material with fraction I protein was shown by gel electrophoresis in the presence of sodium dodecyl sulfate and immunological properties. The carboxylase and oxygenase activities copurify during crystallization, and the crystalline enzyme lacks copper and iron.

Modification of Rhodospirillum rubrum ribulose bisphosphate carboxylase with pyridoxal phosphate. 1. Identification of a lysyl residue at the active site

Ribulose 1,5-bisphosphate carboxylase isolated from Rhodospirillum rubrum was strongly inhibited by low concentrations of pyridoxal 5'-phosphate. Activity was protected by the substrate ribulose bisphosphate and to a lesser extent by other phosphorylated compounds. Pyridoxal phosphate inhibition was enhanced in the presence of magnesium and bicarbonate, but not in the presence of either compound alone. Concomitant with inhibition of enzyme activity, pyridoxal phosphate forms a Schiff base with the enzyme which is reversible upon dialysis and reducible with sodium borohydride. Subsequent to reduction of the Schiff base with tritiated sodium borohydride, tritiated N6-pyridoxyllysine could be identified in the acid hydrolysate of the enzyme. Only small amounts of this compound were present when the reduction was performed in the presence of carboxyribitol bisphosphate, an analogue of the intermediate formed during the carboxylation reaction. Therefore, it is concluded that pyridoxal phosphate modifies a lysyl residue close to or at the active site of ribulose bisphosphate carboxylase.

Mechanism of action of ribulose bisphosphate carboxylase/oxygenase

RuBP carboxylase-oxygenase appears to catalyze carboxylation and oxygenation by homologous mechanisms. A common binding site exists on the enzyme for the acceptor substrate, RuBP. A mechanism is proposed whereby RuBP is isomerized, and a carbanion is generated at C2. Then, either CO2 or O2 is added as an electrophile at C2 to form the corresponding 3-keto-2-carboxy-RBP or 3-keto-2-hydroperoxy-RBP adduct. Hydrolytic cleavage at the C2-C3 bonds of these intermediates by the enzyme is envisioned to produce 2 molecules of 3-phosphoglycerate in the carboxylation sequence and 1 molecule of phosphoglycolate and 1 molecule of 3-phosphoglycerate in the oxygenation sequence. Further work will be necessary to establish the validity of the proposed mechanism.

Ribulose biophosphate carboxylase from Thiobacillus A2. Its purification and properties

Ribulose bisphosphate carboxylase (EC 4.1.1.39) from Thiobacillus A2 has been purified to homogeneity on the basis of polyacrylamide gel electrophoresis and U.V. analysis during sedimentation velocity studies. The enzyme had an optimum pH of about 8.2 with Tris-HCl buffers. The molecular weight was about 521000 with an Srel. of 16.9. Km for RuBP was 122 muM, for total "CO2" it was 4.17 mM, and for Mg2+ 20.0 muM. The absolute requirement for a divalent cation was satisfied by Mg2+ which was replaceable to a certain extent by Mn2+. Activity was not significantly affected by SO(2-4), SO(2-3), or S(2)O(2-3) at 1.0 mM. At this concentration S(2-) caused a 27% stimulation. All mercurials tested were inhibitory. pHMB was the most potent causing about 60% inhibition at 0.04 mM. This inhibition was reversible by low concentrations of cysteine. Cyanide was also inhibitory. Its mode of inhibition with respect to RuBP was un-competitive and with a Ki of 20 muM. Lost activity could be restored partially by GSH or Cu2+. Although azide at the concentration tested had no significant effect on enzyme activity, 2, 4-dinitrophenol at 1.0 mM caused 91% inhibition. Finally, activity was also affected by energy charge.