Nitrogenase. VI. Acetylene reduction assay: Dependence of nitrogen fixation estimates on component ratio and acetylene concentration.

Acetylene reduction, an assay for nitrogenase activity (nitrogen:(acceptor) oxidoreductase, EC 1.7.99.2), Is dependent on the ratio of the two protein components of nitrogenase as well as on C2H2 concentration. As the component I : component II ratio (based on activity) is increased, the C2H2 reduction : N2 fixation ratio decreases to a minimum of 3.4 and then increases. The minimum is found at a ratio near 1 : 1. At a component I : component II ratio of 20 : 1, the C2H2 reduction : N2 fixation ratio is 5.3. Acetylene exhibits substrate inhibition in assays for nitrogenase activity. Both the apparent Km and Ki for acetylene vary as a function of the relative concentrations of components I and II present in the assay. When the more labile component II is limiting in the assay and "saturating" levels of C2H2 (above 0.1 atm) are used, N2-fixation capacity may be greatly under-estimated.     

Hydrogen Effect on Nitrogenase (C2H2 Reduction) Response to Oxygen in Bradyrhizobium japonicum-Phaseoleae Symbioses

The influence of hydrogenase in Bradyrizobum-Phaseoleae symbioseswas studied ex-planta and in-planra in soybean (Glycine max)and cowpea (Vigna unguiculata). The hydrogenase was activatedby the addition of hydrogen in the incubation gas phase whichmodified the response of nitrogenase activity of Hup⁺ (hydrogenuptake positive) symbiosis to the external oxygen partial pressure.For bacteroids the hydrogenase expression increased nitrogenaseactivity at supraoptimal pO₂, acting possibly as a respiratoryprotection of nitrogenase. However, at suboptimal pO₂, nitrogenaseactivity of Hup⁺ bacteroids decreased with hydrogen, a phenomenonattributed to the lower efficiency of ATP synthesis from hydrogenthan from carbon substrates oxidation. For undisturbed nodules,the hydrogenase expression in soybean increased the optimalpO₂ for ARA (COP), from 35.3 to 40.3 kPa O₂, and the ARA atsupraoptimal pO₂; at suboptimal PO₂ there was a negative effectof hydrogenase on ARA, although this inhibition was less thanon bacteroids and was not detected if plants were grown at 15°C rather than 20 °C root temperature. No H₂ effectwas detected on cowpea nodules. The results on soybean nodulesare consistent with the concept that symbiotic nitrogen fixationis oxygen-limited and that hydrogenase activity has no beneficialeffect on nitrogen fixation in O₂ limitation. Key words: Glycine max, hydrogenase, nitrogenase, nitrogen fixation, nodules, Vigna unguiculata     

Cooperative binding of ATP and RNA substrates to the DEAD/H protein DbpA

Unlike most DEAD/H proteins, the purified Escherichia coli protein DbpA demonstrates high specificity for its 23S rRNA substrate in vitro. Here we describe several assays designed to characterize the interaction of DbpA with its RNA and ATP substrates. Electrophoretic mobility shift assays reveal a sub-nanomolar binding affinity for a 153 nucleotide RNA substrate (R153) derived from the 23S rRNA. High affinity RNA binding requires both hairpin 92 and helix 90, as substrates lacking these structures bind DbpA with lower affinity. AMPPNP inhibition assays and ATP/ADP binding assays provide binding constants for ATP and ADP to DbpA with and without RNA substrates. These data have been used to describe a minimal thermodynamic scheme for the binding of the RNA and ATP substrates to DbpA, which reveals cooperative binding between larger RNAs and ATP with cooperative energies of approximately 1.3 kcal mol(-1). This cooperativity is lost upon removal of helix 89 from R153, suggesting this helix is either the preferred target for DbpA's helicase activity or is a necessary structural element for organization of the target site within R153.     

Nitrogenase of Klebsiella pneumoniae. Purification and properties of the component proteins

1. Nitrogenase from the facultative anaerobe Klebsiella pneumoniae was resolved into two protein components resembling those obtained from other nitrogen-fixing bacteria. 2. Both proteins were purified to homogeneity as shown by the criteria of disc electrophoresis and ultracentrifugal analysis. 3. The larger component had a mol.wt. of 218000 and contained one Mo atom, 17Fe atoms and 17 acid-labile sulphide groups/mol; it contained two types of subunit, present in equal amounts, of mol.wts. 50000 and 60000. All the common amino acids were present, with a predominance of acidic residues. The apparent partial specific volume was 0.73; ultracentrifugal analysis gave s⁰_20,w=11.0S and D⁰_20,w=4.94×10⁻⁷cm²/s. The specific activities (nmol of product formed/min per mg of protein) when assayed with the second nitrogenase component were 1500 for H₂ evolution, 380 for N₂ reduction, 1200 for acetylene reduction and 5400 for ATP hydrolysis. The reduced protein showed electron-paramagnetic-resonance signals at g=4.3, 3.7 and 2.015; the Mössbauer spectrum of the reduced protein consisted of at least three doublets. The u.v. spectra of the oxidized and reduced proteins were identical. On oxidation the absorbance increased generally throughout the visible region and a shoulder at 430nm appeared. The circular-dichroism spectra of both the oxidized and reduced proteins were the same, consisting mainly of a negative trough at 220nm. 4. The smaller component had mol.wt. 66800 and contained four Fe atoms and four acid-labile sulphide groups in a molecule comprising two subunits each of mol.wt. 34600. All common amino acids except tryptophan were present, with a predominance of acidic residues. The apparent partial specific volume calculated from the amino acid analysis was 0.732, which was significantly higher than that obtained from density measurements (0.69); ultracentrifugal analysis gave s⁰_20,w=4.8S and D⁰_20,w=5.55×10⁻⁷cm²/s. The specific activities (nmol of product formed/min per mg of protein) were 1050 for H₂ evolution, 275 for N₂ reduction, 980 for acetylene reduction and 4350 for ATP hydrolysis. The protein was not cold-labile. The reduced protein showed electron-paramagnetic-resonance signals in the g=1.94 region. The Mössbauer spectrum of the reduced protein consisted of a doublet at 77°K. The u.v. spectra of reduced and O₂-inactivated proteins were identical, and inactivation by O₂ generally increased the absorbance in the visible region and resulted in a shoulder at 460nm. The circular-dichroism spectra exhibited a negative trough at 220nm and inactivation by O₂ decreased the depth of the trough. 5. The reduction of N₂ and acetylene, and H₂ evolution, were maximal at a 1:1 molar ratio of the Fe-containing protein to the Mo–Fe-containing protein; excess of the Mo–Fe-containing protein was inhibitory. All reductions were accompanied by H₂ evolution. The combined proteins had no ATP-independent hydrogenase activity.     

Nitrogenase from Bacillus polymyxa. Purification and properties of the component proteins.

A purification procedure is described for the components of Bacillus polymyxa nitrogenase. The procedure requires the removal of interfering mucopolysaccharides before the two nitrogenase proteins can be purified by the methods used with other nitrogenase components. The highest specific activities obtained were 2750 nmol C2H4 formed . min-1 . mg-1 MoFe protein and 2521 nmol C2H4 formed . min-1 . mg-1 Fe protein. The MoFe protein has a molecular weight of 215 000 and contains 2 molybdenum atoms, 33 iron atoms and 21 atoms of acid-labile sulfur per protein molecule. The Fe protein contains 3.2 iron atoms and 3.6 acid-labile sulfur atoms per molecule of 55 500 molecular weight. Each Fe protein binds two ATP molecules. The EPR spectra are similar to those of other nitrogenase proteins. MgATP changes the EPR of the Fe protein from a rhombic to an axial-type signal.     

Nitrogenase of Klebsiella pneumoniae. Distinction between proton-reducing and acetylene-reducing forms of the enzyme: effect of temperature and component protein ratio on substrate-reduction kinetics.

Non-linear rates of acetylene reduction and concomitant H2 evolution were observed for the nitrogenase of Klebsiella pneumoniae at 10 degrees C. A lag phase of 1-4 min, dependent on the ratio of Mo-Fe protein to Fe protein present, occurred before linear rates of acetylene reduction were achieved. A complementary burst phase for concomitant H2 evolution in the presence of acetylene was also observed. When the proton was the only reducible substrate present, linear rates of H2 evolution were observed. N2 was a poor substrate under these conditions. Similar lag and burst phases occurred at 30 degrees C, but only when a large molar excess of Mo-Fe protein with respect to Fe protein was present. The results at 10 degrees C show that the binding of acetylene to the enzyme stimulates electron flow, but that these electrons, which initially reduce protons, can only reduce acetylene after a lag phase that cannot be accommodated in the turnover time calculated under steady-state conditions.     

Nitrogenase from Azotobacter chroococcum. Purification and properties of the component proteins.

1. A large-scale purification of the nitrogenase components from Azotobacter chroococcum yielded two non-haem iron proteins, both of which were necessary for nitrogenase activity and each had a specific activity of approximately 2000 +/- 300 nmol of acetylene reduced/mg protein per min in the presence of sautrating amounts of the other. This procedure freed the Mo-Fe protein from a protein contaminant which had an electron paramagnetic resonance signal at g = 1.94. 2. Both proteins were purified to homogeneity as determined by disc gel electrophoresis and ultracentrifugal analysis. Both proteins were oxygen-sensitive but not cold-labile. Ultracentrifugal analysis indicated that both proteins dissociated to a slight degree at concentrations below 2 mg/ml. 3. The larger of the two proteins had a molecular weight of 227 000 and contained 1.9 +/- 0.3 atoms of Mo, 23 +/- 2 atoms of Fe, 20 +/- 2 acid-labile sulphide and 47 tryptophan residues/mol. The protein consists of 4 subunits of mol. wt 60 000 (approx.). The reduced protein showed electron paramagmetic resonance signals at g = 4.29, 3.65 and 2.013 but not in the area of g = 5 to 6. Upon oxidation abosrbance increased throughout the visible region of the ultraviolet visible spectrum, with a maximum difference between oxidised and reduced protein occurring at 430 nm. 4. The smaller protein had a molecular weight of 64 000 and contained 4 g-atoms of Fe and 4 acid-labile sulphide groups/mol but no tryptophan. It had two subunits of mol. wt 30 800. The reduced protein showed electron paramagnetic resonance signhe protein retained almost full activity after oxidation with phenazine methosulphate. The ultraviolet visible spectrum of oxidised protein was clearly different from that of the oxygen-inactivated protein: it had a sharp peak at 269 nm and a broad absorbance between 340 and 470 nm with a maximum difference between oxidised and reduced forms at 430 nm. Oxygen-inactivated protein showed a sharp peak at 277.5 nm and broad peaks from 305 to 360, 400 to 425 and 435 to 475 nm. 5. Amino acid analyses of both proteins showed that most common amino acids were present with a preponderance of acidic residues. Analyses of compositional relatedness showed that the nitrogenase proteins from A. chroococcum were most closely related to those from A. vinelandii and least so to those from Clostridium pasteurianum.     

Nitrogenase of Klebsiella pneumoniae. Interaction of the component proteins studied by ultracentrifugation

Sedimentation-velocity analyses of mixtures of the component proteins of nitrogenase of Klebsiella pneumoniae at a 1:1 molar ratio, showed a single peak of sedimentation coefficient (12.4S) considerably greater than that obtained for the larger (Fe+Mo-containing) protein centrifuged alone (10.4S). When the ratio exceeded 1:1 (the smaller Fe-containing protein in excess) an additional peak corresponding in sedimentation coefficient (about 4.5S) to free Fe-containing protein appeared. When proteins, which had been inactivated by exposure to air were used, no interaction occurred. Na(2)S(2)O(4) at 2mm both reversed and prevented interaction between the two proteins; sedimentation coefficients corresponded to those of the proteins when centrifuged alone. These results demonstrate the formation of a complex between the nitrogenase proteins, and, together with data of activity titration curves, are consistent with the formulation of the nitrogenase complex of K. pneumoniae as (Fe-containing protein)-(Fe+Mo-containing protein).     

Effect of MPTP on brain mitochondrial H2O2 and ATP production and on dopamine and DOPAC in the striatum

An experimental rat model of Parkinson's disease was established by injecting rats directly in the striatum with the neurotoxic agent 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). In order to study the action mechanism of this neurotoxic agent, MPTP and its main metabolite 1-methyl-4-phenylpyridinium (MPP+) were also added to suspensions of pyruvate/malate-supplemented nonsynaptic brain mitochondria, and the rates of hydrogen peroxide and ATP production were measured. Intrastriatal administration of MPTP produced a pronounced decrease in striatal dopamine levels (p < 0.005) and a strong increase in 3,4-hydroxiphenylacetic acid/dopamine ratio (an indicator of dopamine catabolism; p < 0.005) in relation to controls, as evaluated by in situ microdialysis. MPTP addition to rat brain mitochondria increased hydrogen peroxide production by 90%, from 1.37+/-0.35 to 2.59+/-0.48 nanomoles of H2O2/minute . mg of protein (p < 0.01). The metabolite MPP+ produced a marked decrease on the rate of ATP production of brain mitochondria (p < 0.005). These findings support the mitochondria-oxidative stress-energy failure hypothesis of MPTP-induced brain neurotoxicity.     

The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio

Members of the FoF1, AoA1 and VoV1 family of ATP synthases and ATPases have undergone at least two reversals in primary function. The first was from a progenitor proton-pumping ATPase to a proton-driven ATP synthase. The second involved transforming the synthase back into a proton-pumping ATPase. As proposed earlier [FEBS Lett. 259 (1990) 227], these reversals required changes in the H+/ATP coupling ratio from an optimal value of about 2 for an ATPase function to about 4 for an ATP synthase function. The doubling of the ratio that occurred at the ATPase-to-Synthase transition was accomplished by duplicating the gene that encodes the nucleotide-binding catalytic subunits followed by loss of function in one of the genes. The halving of the ratio that occurred at the Synthase-to-ATPase transition was achieved by a duplication/fusion of the gene that encodes the proton-binding transporter subunits, followed by a loss of function in one half of the double-sized protein. These events allowed conservation of quaternary structure, while maintaining a sufficient driving force to sustain an adequate phosphorylation potential or electrochemical gradient. Here, we describe intermediate evolutionary steps and a fine-tuning of the H+/ATP coupling ratio to optimize synthase function in response to different environments. In addition, we propose a third reversal of function, from an ATPase back to an ATP synthase. In contrast to the first two reversals which required a partial loss in function, the change in coupling ratio required for the third reversal is explained by a gain in function.     

ATP analogs substituted on the 2-position as substrates for dynein ATPase activity

In contrast to previously studied ATP analogs, the two-substituted ATP analogs, 2-N3 ATP and 2-Cl ATP were good substrates for dynein ATPase. The Vmax for hydrolysis of both analogs was significantly higher than for ATP and the Km for both analogs was comparable to ATP. The higher hydrolytic rate for the analogs might be explained by a faster dissociation rate of the diphosphate product. This interpretation is supported by measurements of the dissociation rate of the inhibitor, vanadate. The estimate dissociation rate of vanadate with the analogs as substrate is approx. 2-fold higher than with ATP as substrate. These data together with previous studies on a variety of ATP analogs suggest that the 6-amino group on adenine is important for recognition by dynein and that the anti-conformation of the adenine, favored by 2-substituents, is the favored conformation of the nucleotide.     

Proton translocation and ATP formation coupled to electron transport from H2O to the primary acceptor of photosystem 2.

1. The rate of electron transport from H2O to silicomolybdate in the presence of 3-(3-4-dichlorophenyl)-1,1-dimethylurea (diuron) (which involves the oxygen-evolving enzyme, the photochemistry of photosystem 2 and the primary electron acceptor of photosystem 2) is controlled by internal pH. This is based on the shift of the pH profile of the rate of electron transport upon addition of uncouplers, or by using EDTA-treated chloroplasts. Both stimulation and inhibition of electron transport by addition of uncouplers (depending on external pH) could be observed. These effects are obtained in the diuron-insensitive photoreductions of either silicomolybdate or ferricyanide. These experiments provide strong evidence that a proton translocating site exists in the sequence of the electron transport H2O leads to Q (the primary acceptor of photosystem 2). 2. The photoreduction of silicomolybdate in the presence of diuron causes the formation of delta pH. The value of delta pH depends on the external pH and its maximal value was shown to be 2.4. The calculated internal pH at different external pH values was found to be rather constant, namely between 5.1 -- 5.2. 3. Electron transport from H2O to silicomolybdate (in the presence of diuron) does not support ATP formation. It is suggested that this is due to the fact that the delta pH formed is below the "threshold" delta pH required for the synthesis of ATP. By adding an additional source of energy in the form of a dark diffusion potential created in the presence of K+ and valinomycin, significant amounts of ATP are formed in this system.     

H+/ATP ratio of proton transport-coupled ATP synthesis and hydrolysis catalysed by CF0F1-liposomes

The H(+)/ATP ratio and the standard Gibbs free energy of ATP synthesis were determined with a new method using a chemiosmotic model system. The purified H(+)-translocating ATP synthase from chloroplasts was reconstituted into phosphatidylcholine/phosphatidic acid liposomes. During reconstitution, the internal phase was equilibrated with the reconstitution medium, and thereby the pH of the internal liposomal phase, pH(in), could be measured with a conventional glass electrode. The rates of ATP synthesis and hydrolysis were measured with the luciferin/luciferase assay after an acid-base transition at different [ATP]/([ADP][P(i)]) ratios as a function of deltapH, analysing the range from the ATP synthesis to the ATP hydrolysis direction and the deltapH at equilibrium, deltapH (eq) (zero net rate), was determined. The analysis of the [ATP]/([ADP][P(i)]) ratio as a function of deltapH (eq) and of the transmembrane electrochemical potential difference, delta micro approximately (H)(+) (eq), resulted in H(+)/ATP ratios of 3.9 +/- 0.2 at pH 8.45 and 4.0 +/- 0.3 at pH 8.05. The standard Gibbs free energies of ATP synthesis were determined to be 37 +/- 2 kJ/mol at pH 8.45 and 36 +/- 3 kJ/mol at pH 8.05.     

Effect of alkaline and saline substrates on ABA contents,distribution and transport in plant roots

The distribution of the phytohormone abscisic acid (ABA) between plant and soil and within plants growing on an alkaline substrate has been studied in order to separate the true effect of high soil pH from any effects that might be a result of the high salinity normally observed in alkaline soils. Leaves of a range of plants grown in an alkaline and saline solid substrate (municipal solid waste incinerator bottom slag) exhibited higher ABA levels than leaves of control plants. In contrast, roots of most plants grown on alkaline and saline substrates, particularly those without an exodermis (various species of Fabaceae), had slightly lower than or comparable ABA contents to control roots. However, in corn roots (Zea maysL. cv. Garant FAO 240) which possess a well-developed exodermis, alkaline and saline conditions in the rhizosphere did not reduce the endogenous ABA concentration, because the leaching of ABA from corn roots into the rhizosphere was lower than that from Vicia faba (variety Dreifache Weisse) roots. ABA efflux from corn and Vicia roots into the soil solution was observed only during the first days of the experiments and thereafter became substantially decreased. Because the leaching of ABA from Vicia faba roots into the rhizosphere was higher than that from corn roots, the leaves of Vicia plants grown in alkaline soil at low salinity no longer exhibited an elevated ABA concentration. However, whilst the roots of corn plants grown on desalted slag retained ABA levels that were higher than those of the control, the ABA content of leaves was not significant higher than the controls. For this reason, root ABA retention must be enough to induce tolerance to alkalinity in corn plants and there is no need to implicate changes in ABA concentrations in the aerial parts of the plant as having a role in this tolerance. In alkaline soil substrates, considerable portions of the ABA synthesised in the roots leached out into the soil solution of the rhizosphere according to the anion trap concept. An exodermis substantially reduces this leakage. The transient nature of ABA efflux into the rhizosphere was a result of the fact that the salt stress itself was only a transient phenomenon due to a washout of salt by irrigation. The results match predictions of mathematical models describing the effect of alkaline pH on the distribution of abscisic acid within plants and between roots and the rhizosphere. Species that can retain root ABA in the face of its tendency to leach into the more alkaline compartment are able to tolerate these normally harmful sites. This revised version was published online in June 2006 with corrections to the Cover Date.     

Nitrogenase Activity (C2H2) of Isolated Peanut and Cowpea Bacteroids under Nitrogen, Argon, and Helium Atmospheres

Peanut nodules have been reported to have several times highernitrogenase activity (C₂H₂) than cowpea and siratro nodulesinduced by the same rhizobial strains. The unique morphologicalmodification of the peanut bacteroids has been considered tobe the cause for such enhanced activity. To investigate thispossibility, nitrogenase activities of isolated peanut and cowpeabacteroids were compared. Peanut bacteroids showed low initialrates of C₂H₂ reduction which increased with time, but for cowpeabacteroids higher initial rates decreased with time. Moreover,the gases used as diluent for O₂ (N₂, Ar, or He) were foundto influence O₂ tolerance and C₂H₂-reduction rates of bacteroids.