Particle density and protein composition of the peribacteroid membrane from soybean root nodules is affected by mutation in the microsymbiont Bradyrhizobium japonicum

Particle frequency of the peribacteroid membrane (PBM) from nodules of Glycine max (L.) Merr. cv. Maple Arrow infected with Bradyrhizobium japonicum 61-A-101 (wild-type strain) was determined by freeze-fracturing to be about 2200·m^-2 in the protoplasmic fracture face and 700·m^-2 in the exoplasmic fracture face. In membranes isolated from nodules infected with the mutant RH 31-Marburg of B. japonicum, the particle frequency was similar in both fracture faces with 1200–1300 particles·m^-2. Analysis of particlesize distribution on peribacteroid membranes showed a loss, especially of particle sizes larger than 11 nm, in the mutant-infected nodules. Two-dimensional gel electrophoresis (isoelectric focussing and sodium dodecyl sulfate-polyacrylamide) showed 27 different polypeptides in the PBM from nodules infected with the wild-type strain, four of which were absent from the PBM of nodules infected with the mutant RH 31-Marburg, which also exhibited one extra small-molecular-weight polypeptide. At least 14 of the 27 polypeptides in the PBM from the wild-type-infected nodule were glycoproteins. In three of these glycoproteins, post-translational modifications were either lacking or different when the membrane was derived from mutant-infected nodules.Abbreviations EF exoplasmatic fracture face - HRPO horse radish peroxidase - IEF Isoelectric focussing - PBM peribacteroid membrane - PF protoplasmatic fracture face - PNA peanut agglutinin - PSA Pisum sativum agglutinin - SDS-PAGE Sodium dodecyl sulfate-polyacrylamide gel electrophoresis     

Proton density and apoplastic domains within soybean nodules in relation to the oxygen diffusion barrier

A spin-echo pulse sequence was used to obtain ¹H nuclear magnetic resonance microimages of soybean nodules, with resolution to 40 mm and 3D presentation. At an acquisition time (TR) of c. 270 ms and a short echo time (TE) of 8.3 ms, a high proton intensity was detected in infected tissue and vascular strands, relative to the cortex. A longer TE of 15.5 ms was associated with a relatively low proton intensity in infected tissue. Thus protons in infected tissue were characterized by a short T₂. Following detopping of the plant, or treatment of the root system with Ar:O₂, proton intensity (TE 5.9, TR 120 ms) decreased exponentially in a zone corresponding to the inner cortex-outer infected region. This result is interpreted as being caused by a loss of water mobility (i.e. increase in viscosity) or a filling of intercellular air spaces with fluid (i.e. loss of air-water interfaces). The membrane impermeant tracer lucifer yellow was observed to infiltrate from the rhizosphere through the nodule cortex into the infected region in intact nodules of detopped and Ar:O₂-treated, but not control, plants. This result is consistent with the filling of air spaces with fluid following the imposed treatments, allowing infiltration of aqueous tracers. Variation in intercellular air space volume within the inner cortex has been suggested as a mechanism to allow a variable rate of diffusion of O₂ into soybean nodules.     

Aldrin epoxidase from soybean root nodules

Soybean (Glycine max cv Forrest) root nodule homogenates oxidized aldrin to its epoxide, dieldrin. In crude tissue brei, addition of an NADPH-generating system was inhibitory to epoxidation. However, anaerobic gel filtration and sucrose density separation removed factors required for inhibition by NADPH, allowing a normal stimulation by the NADPH-generating system. In fractions from sucrose density gradients, activity was found predominantly at a density containing rough microsomes, with additional activities in the soluble and other fractions. Epoxidase activity was 2–4-times greater in the nitrogen-fixing nodules than in roots. This demonstration of active epoxidation indicates the capacity of nodules to detoxify other pesticides and xenobiotics.     

Morphological and physiological response of soybean treated with the microsymbiont Bradyrhizobium japonicum pre-incubated with genistein

Genistein, a major root-secreted isoflavone of soybean (Glycine max (L.) Merr), is critical for the legume-Bradyrhizobium symbiosis as it induces several bacterial nod-gene systems. An experiment with soybean grown under salt stress was conducted to evaluate the effect of exogenous genistein addition to the Bradyrhizobium culture medium on subsequent nodulation, nitrogen fixation and selected plant physiological attributes. Five day-old plants (in pots) were inoculated with a liquid B. japonicum broth culture and irrigated with B&D solution containing either 0, 25, 50 and 100 mM NaCl. Four weeks after inoculation, maximum photochemical efficiency of PSII (Fv/Fm), photosynthetic rate, stomatal conductance, and transpiration rate were measured. Number of nodules per plant and apparent nitrogen fixation (as acetylene reduction activity) were determined. Salt stress decreased nodule number/plant and nitrogenase activity/plant and induced large changes of both photosynthetic parameters and antioxidant enzyme activity, compared to the control, genistein reversed the effect in each level of salinity tested. Moreover, pre-treatment of the microsymbiont with genistein enhanced maximum photochemical efficiency, photosynthetic rate, stomatal conductance and transpiration rate, while the enzymatic activities of catalase, superoxide dismutase and peroxidase in leaves and roots were not affected. It can be concluded that preincubation of the B. japonicum inoculant with genistein probably contributed towards growth in soybean via enhancement of nodulation and nitrogen fixation under both normal and salt stress conditions.     

Ferric leghemoglobin reductase from soybean root nodules

An NADH: (acceptor) oxidoreductase from the cytosol of soybean root nodules was purified by ammonium sulfate fractionation, hydroxylapatite adsorption, and Sephacryl S-200 Superfine chromatography. The native molecular weight of the reductase was found to be 100,000 by analytical gel filtration and 83,000 by equilibrium ultracentrifugation. The subunit molecular weight was 54,000 as determined by sodium dodecyl sulfate-polyacrylamide slab gel electrophoresis. The pI of the enzyme was 5.5. With ferric leghemoglobin (Lb) as the substrate, nearly identical initial velocities were obtained using either CO or O2 to ligate the enzymatically produced ferrous leghemoglobin. With CO as the ligand in the reaction, the product of the enzyme-catalyzed, NADH-dependent reduction of ferric Lb was spectrally identified as LbCO. Initial velocity was a linear function of increasing enzyme concentration. NADPH was only 31% as effective an electron donor as NADH as determined by initial velocity. The Michaelis constants (Km) for ferric Lba and NADH were 9.5 and 18.8 microM, respectively. Myoglobin, Lba, Lbc1, Lbc2, Lbc3, and Lbd were reduced at similar rates by the reductase. At pH 5.2, acetate-bound ferric Lb and nicotinate-bound ferric Lb were reduced by the enzyme at 83 and 5%, respectively, of rates observed in the absence of these ligands. The rate of enzymatic reduction of ferric Lb was constant between pH 6.5 and 7.6 but increased approximately threefold at pH 5.2. The results indicate that the NADH: (acceptor) oxidoreductase could be identified as a ferric Lb reductase.     

Flavin-mediated reduction of ferric leghemoglobin from soybean nodules

The reduction of ferric leghemoglobin (Lb³⁺) from soybean (Glycine max (L.) Merr.) nodules by riboflavin, FMN and FAD in the presence of NAD(P)H was studied in vitro. The system NAD(P)H + flavin reduced Lb³⁺ to oxyferrous (Lb²⁺ · O₂) or deoxyferrous (Lb²⁺) leghemoglobin in aerobic or anaerobic conditions, respectively. In the absence of O₂ the reaction was faster and more effective (i.e. less NAD(P)H oxidized per mole Lb³⁺ reduced) than in the presence of O₂; this phenomenon was probably because O₂ competes with Lb³⁺ for reductant, thus generating activated O₂ species. The flavin-mediated reduction of Lb³⁺ did not entail production of superoxide or peroxide, indicating that NAD(P)H-reduced flavins were able to reduce Lb³⁺ directly. The NAD(P)H + flavin system also reduced the complexes Lb³⁺ · nicotinate and Lb³⁺ · acetate to Lb²⁺ · O₂, Lb²⁺ or Lb²⁺ · nicotinate, depending on the concentrations of ligands and of O₂. In the presence of 200 M nitrite most Lb remained as Lb³⁺ in aerobic conditions but the nitrosyl complex (Lb²⁺ · NO) was generated in anaerobic conditions. The above-mentioned characteristics of the NAD(P)H + flavin system, coupled with its effectiveness in reducing Lb³⁺ at physiological levels of NAD(P)H and flavins in soybean nodules, indicate that this mechanism may be especially important for reducing Lb³⁺ in vivo.Abbreviations and Terminology FLbR ferric leghemoglobin reductase - Hb²⁺ /Hb³⁺ hemoglobin containing Fe²⁺ /Fe²⁺ - Lb²⁺ /Lb³⁺ leghemoglobin containing Fe²⁺ /Fe³⁺ - Lb³⁺ · nicotinate/acetate Lb in which nicotinate or acetate are complexed to Lb³⁺ - Lb²⁺ · O₂/CO/NO/nicotinate Lb in which O₂, CO, NO or nicotinate are complexed to Lb²⁺ - Rfl riboflavin - SOD superoxide dismutase (EC 1.15.1.1) Published as Paper No. 9237, Journal Series, Nebraska Agricultural Research DivisionWe thank M.B. Crusellas for his skillful drawings. M. Becana thanks the Spanish Ministry of Education and Science/Fulbright Commission for financial support.     

Hexose kinases from the plant cytosolic fraction of soybean nodules

The enzymes responsible for the phosphorylation of hexoses in the plant cytosolic fraction of soybean (Glycine max L. Merr cv Williams) nodules have been studied and a hexokinase (ATP:d-hexose 6-phosphotransferase EC 2.7.1.1) and fructokinase (ATP:d-fructose 6-phosphotransferase EC 2.7.1.4) shown to be involved. The plant cytosolic hexokinase had optimum activity from pH 8.2 to 8.9 and the enzyme displayed typical Michaelis-Menten kinetics. Hexokinase had a higher affinity for glucose (K_m 0.075 millimolar) than fructose (K_m 2.5 millimolar) and is likely to phosphorylate mainly glucose in vivo. The plant cytosolic fructokinase had a pH optimum of 8.2 and required K⁺ ions for maximum activity. The enzyme was specific for fructose (apparent K_m 0.077 millimolar) but concentrations of fructose greater than 0.4 millimolar were inhibitory. The native molecular weight of fructokinase was 84,000 ± 5,000. The roles of these enzymes in the metabolism of glucose and fructose in the host cytoplasm of soybean nodules are discussed.     

Isolation of plant-growth-promoting Bacillus strains from soybean root nodules

Endophytic bacteria reside within plant tissues and have often been found to promote plant growth. Fourteen strains of putative endophytic bacteria, not including endosymbiotic Bradyrhizobium strains, were isolated from surface-sterilized soybean (Glycine max. (L.) Merr.) root nodules. These isolates were designated as non-Bradyrhizobium endophytic bacteria (NEB). Three isolates (NEB4, NEB5, and NEB17) were found to increase soybean weight when plants were co-inoculated with one of the isolates and Bradyrhizobium japonicum under nitrogen-free conditions, compared with plants inoculated with B. japonicum alone. In the absence of B. japonicum, these isolates neither nodulated soybean, nor did they affect soybean growth. All three isolates were Gram-positive spore-forming rods. While Biolog tests indicated that the three isolates belonged to the genus Bacillus, it was not possible to determine the species. Phylogenetic analysis of 16S rRNA gene hypervariant region sequences demonstrated that both NEB4 and NEB5 are Bacillus subtilis strains, and that NEB17 is a Bacillus thuringiensis strain.     

Sucrose synthase of soybean nodules

Sucrose synthase (UDPglucose: d-fructose 2-α-d-glucosyl transferase, EC 2.4.1.13) has been purified from the plant cytosolic fraction of soybean (Glycine max L. Merr cv Williams) nodules. The native enzyme had a molecular weight of 400,000. The subunit molecular weight was 90,000 and a tetrameric structure is proposed for soybean nodule sucrose synthase. Optimum activity in the sucrose cleavage and synthesis directions was at pH 6 and pH 9.5 respectively, and the enzyme displayed typical Michaelis-Menten kinetics. Soybean nodule sucrose synthase had a high affinity for UDP (K_m, 5 micromolar) and a relatively low affinity for ADP (apparent K_m, 0.13 millimolar) and CDP (apparent K_m, 1.1 millimolar). The K_m for sucrose was 31 millimolar. In the synthesis direction, UDPglucose (K_m, 0.012 millimolar) was a more effective glucosyl donor than ADPglucose (K_m, 1.6 millimolar) and the K_m for fructose was 3.7 millimolar. Divalent cations stimulated activity in both the cleavage and synthesis directions and the enzyme was very sensitive to inhibition by heavy metals.     

Genetic differentiation of the Tuva population with respect to the Alu insertions]

Polymorphism of three rural populations of the Tuva Republic was examined using a set of five autosomal Alu insertions at the ACE, PLAT, PV92, APOA1, and F13B loci. The allele frequency distribution patterns revealed in Tuvinians were typical to Mongoloid populations of Asia and were characterized by relatively high frequency of the Alu-repeat insertion at the PV92 and F13B loci along with relatively low insertion frequency at the APOA1 locus. With respect to the test systems used, Tuvinian populations examined displayed high levels of genetic diversity. The mean expected heterozygosity values in the populations of Kugurtug, Toora-Khem, and Teeli were 0.433, 0.407, and 0.437, respectively. The level of genetic diversity in the pooled Tuvinian sample was 0.432. The coefficient of genetic differentiation in the three populations studied was 1.45 pointing to relatively low level of genetic subdivision of the indigenous Tuvinian populations. However, estimates of genetic differentiation of the Tuvinian gene pool made by use of the Alu-repeat system were higher compared to those performed using classical protein systems, mtDNA, or Y-chromosomal haplotypes. Even though Tuvinian populations were characterized by common gene pool, some features specific to Western Tuvinian population could be distinguished. These features could be associated with higher contribution of the Caucasian component to the gene pool of this population. Phylogenetic analysis demonstrated close genetic relationships between the Tuvinian and Altaic ethnic populations.     

Leghaemoglobin within bacteroid-enclosing membrane envelopes from soybean root nodules

Methods are reported for the preparation from soybean (Glycine max (L.) Merr.) root nodules, of well-washed, intact membrane envelopes containing bacteroids. The intact envelopes are of much lower density than the bacteroids within and therefore only low speed centrifugation (approx. 150 g) may be used. The optimum osmotic strength is 600 mOsm/kg H₂O. The envelope contents were recovered following mild osmotic shock and-or hard centrifugal packing at >10,000 g. Extracts prepared in this way contained leghaemoglobin (identified spectrophotometrically), low-molecular-weight fluorescent materials and other components which are yet to be identified. Envelope leghaemoglobin did not react with specific antibody until the envelopes were ruptured. ¹³¹I-Labelled leghaemoglobin or bovine serum albumin, added during initial breakage of nodule cells, was not released when envelopes were ruptured to release leghaemoglobin. It is therefore concluded that this leghaemoglobin is located within the envelope space and did not arise from adhering or occluded cytosol leghaemoglobin. Based on the number and dimensions of microscopically intact envelopes in these preparations, the concentration within that space was in the range 178–523 M. Based on these estimates, leghaemoglobin within envelopes represented about one third of the total amount present in the nodule cells. Flat-bed isoelectric focusing of partially-purified envelope leghaemoglobin demonstrated that the latter contained all of the leghaemoglobin components previously reported for soybean nodules and an additional minor component focusing between leghaemoglobins a and b.     

High-performance liquid chromatographic separation of leghemoglobins from soybean root nodules

A crude fraction of soybean nodule ferri-leghemoglobin was absorbed onto a commercial DEAE HPLC column at pH 8.0, and resolved into eight isoprotein fractions. The identity of the leghemoglobins were determined by their order of elution from the DEAE column and by isoelectric focusing, using isoprotein standards isolated by conventional procedures. The three isoproteins of the c complex, c1, c2, c3, were not resolved. Unexpected heme containing proteins eluted just after leghemoglobin a and the c complex. These components possessed proteins similar to leghemoglobin a and the c complex, respectively, as judged by isoelectric focusing and absorbance spectra of the ferri and ferrous forms. The components designated leghemoglobin a' and leghemoglobin c' were also differentiated from leghemoglobin a and c by reverse-phase HPLC in a C18 column. Amounts of protein for the DEAE HPLC column ranged from 10 micrograms to 20 mg and sample volumes ranged from 2 to 250 microliters. The time required for chromatography varied depending on the gradient used, but never exceeded 40 min for samples up to 5 mg protein or 120 min for samples containing 5 to 20 mg protein. Due to the sensitivity of detection at 403 nm and leghemoglobins being the predominant chromophore at that wavelength, it was possible to quantitate levels of individual leghemoglobins in samples extracted from single nodules (ca. 15 to 65 mg fresh weight tissue). Quantitation was performed by interfacing the spectrophotometer output (10 mV) to a microcomputer and using commercially available software.     

Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules

miRNAs are ～21 nt non-coding RNAs and play important roles in plant development and response to stress. Symbiotic nitrogen fixation (SNF) is agronomically important for reducing the need of nitrogen fertilizers. The soybean root nodule is the place where SNF takes place. To identify miRNAs that are possibly involved in nitrogen fixation in soybean functional nitrogen-fixing nodules, a small library of RNAs was constructed from the functional nodules harvested 28 days after inoculation with rhizobium. Thirty-two small RNA sequences were identified as belonging to 11 miRNA families. Eight miRNAs are conserved across plant species, twenty are specific to soybean, and the four remaining miRNAs are novel. Expression analysis revealed that miRNAs were differentially expressed in the different tissues. Combinatorial miRNA target prediction identified genes that are involved in multiple biological processes. The results suggest that miRNAs play critical and diverse roles in SNF, nutrient acquisition, and plant development.     

Purification and properties of asparagine synthetase from soybean root nodules

Asparagine synthetase was purified 240-fold from soybean (Glycine max (L.) Merr.) root nodules with a final recovery of 5% using Reactive Blue 2-crossed linked Agarose affinity gel chromatography. High levels of sulfhydryl protectants were required and the inclusion to glycerol and substrates in the extraction buffer helped to stabilize the enzyme. The final preparation had a specific activity of 3.77 mkat/kg protein when assayed at 30°C and was free of contaminating asparaginase activity. The enzyme had a broad pH maximum around pH 8.0 and apparent K_m values for the substrates aspartate, Mg · ATP, and glutamine were 1.24 mM, 0.076 mM and 0.16 mM, respectively. Ammonium ion could partially replace glutamine as the nitrogen donor. Initial velocity patterns yielded parallel inverse plots with all substrate pairs suggesting an overall ping-pong reaction mechanism. Product inhibition patterns provided evidence that glutamine was the first substrate to bind to the enzyme and asparagine was the last product released.     

A reexamination of the buoyant density of chicken ribosomal DNA

The buoyant density of chicken rDNA has been determined by means of partial enrichment of DNA into rDNA sequences, molecular rRNA-DNA hybridization of DNA fractions of CsCl gradients and determination, by analytical ultracentrifugation, of the density of the fraction corresponding to the maximum of hybridization. Two hybridization peaks were found, the most important possessing a density of 1.7245 g/ml and the other one, a density of about 1.718 g/ml. The latter is expected to represent the mitochondrial rDNA.