Effects of plant growth promoting rhizobacteria (PGPR) on rooting and root growth of kiwifruit (Actinidia deliciosa) stem cuttings.

The effects of plant growth promoting rhizobacteria (PGPR) on the rooting and root growth of semi-hardwood and hardwood kiwifruit stem cuttings were investigated. The PGPR used were Bacillus RC23, Paenibacillus polymyxa RC05, Bacillus subtilis OSU142, Bacillus RC03, Comamonas acidovorans RC41, Bacillus megaterium RC01 and Bacillus simplex RC19. All the bacteria showed indole-3-acetic acid (IAA) producing capacity. Among the PGPR used, the highest rooting ratios were obtained at 47.50% for semi-hardwood stem cuttings from Bacillus RC03 and Bacillus simplex RC19 treatments and 42.50% for hardwood stem cuttings from Bacillus RC03. As well, Comamonas acidovorans RC41 inoculations indicated higher value than control treatments. The results suggest that these PGPR can be used in organic nursery material production and point to the feasibility of synthetic auxin (IBA) replacement by organic management based on PGPR.

Effects of plant growth promoting rhizobacteria (PGPR) on rooting and root growth of kiwifruit (Actinidia deliciosa) stem cuttings

The effects of plant growth promoting rhizobacteria (PGPR) on the rooting and root growth of semi-hardwood and hardwood kiwifruit stem cuttings were investigated. The PGPR used were Bacillus RC23, Paenibacillus polymyxa RC05, Bacillus subtilis OSU142, Bacillus RC03, Comamonas acidovorans RC41, Bacillus megaterium RC01 and Bacillus simplex RC19. All the bacteria showed indole-3-acetic acid (IAA) producing capacity. Among the PGPR used, the highest rooting ratios were obtained at 47.50 percent for semi-hardwood stem cuttings from Bacillus RC03 and Bacillus simplex RC19 treatments and 42.50 percent for hardwood stem cuttings from Bacillus RC03. As well, Comamonas acidovorans RC41 inoculations indicated higher value than control treatments. The results suggest that these PGPR can be used in organic nursery material production and point to the feasibility of synthetic auxin (IBA) replacement by organic management based on PGPR.

Biosynthesis and native granule characteristics of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in Delftia acidovorans.

The ability of Delftia acidovorans to incorporate a broad range of 3-hydroxyvalerate (3HV) monomers into polyhydroxyalkanoate (PHA) copolymers was evaluated in this study. Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] containing 0-90 mol% of 3HV was obtained when a mixture of sodium 3-hydroxybutyrate and sodium valerate was used as the carbon sources. Transmission electron microscopy analysis revealed an interesting aspect of the P(3HB-co-3HV) granules containing high molar ratios of 3HV whereby, the copolymer granules were generally larger than those of poly(3-hydroxybutyrate) [P(3HB)] granules, despite having almost the same cellular PHA contents. The large number of P(3HB-co-3HV) granules occupying almost the entire cell volume did not correspond to a higher amount of polymer by weight. This indicated that the granules of P(3HB-co-3HV) contain polymer chains that are loosely packed and therefore have lower density than P(3HB) granules. It was also interesting to note that a decrease in the length of the side chain from 3HV to 4-hydroxybutyrate (4HB) corresponded to an increase in the density of the respective PHA granules. The presence of longer side chain monomers (3HV) in the PHA structure seem to exhibit steric effects that prevent the polymer chains in the granules from being closely packed. The results reported here have important implications on the maximum ability of bacterial cells to accumulate PHA containing monomers with longer side chain length.

High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32.

The porin Omp32 is the major outer membrane protein of the bacterium Delftia acidovorans. The crystal structures of the strongly anion-selective porin alone and in complex with the substrate malate were solved at 1.5 and 1.45 A resolution, respectively, and revealed a malate-binding motif adjacent to the channel constriction zone. Binding is mediated by interaction with a cluster of two arginine residues and two threonines. This binding site is specific for Omp32 and reflects the physiological adaptation of the organism to organic acids. Structural studies are combined with a 7-ns unbiased molecular dynamics simulation of the trimeric channel in a model membrane. Molecular dynamics trajectories show how malate ions are efficiently captured from the surrounding bulk solution by the electrostatic potential of the channel, translocated to the binding site region, and immobilized in the constriction zone. In accordance with these results, conductance measurements with Omp32 inserted in planar lipid membranes revealed binding of malate. The anion-selective channel Omp32 is the first reported example of a porin with a 16-stranded beta-barrel and proven substrate specificity. This finding suggests a new view on the correlation of porin structure with substrate binding in specific channels.

Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins.

The functional properties of the anion-selective porin Omp32 from the bacterium Delftia acidovorans, formerly Comamonas acidovorans, are determined by the particularly narrow channel constriction and the electrostatic field inside and outside the pore. A cluster of arginines (Arg 38, Arg 75, and Arg 133) determines the electrostatic field close to the constriction zone. Stacked amino acids carrying charges are prone to drastic pK(a) shifts. However, optimized calculations of the titration behavior of charged groups, based on the finite-difference Poisson-Boltzmann technique, suggest that all the arginines are charged at physiological pH. Protonation of the clustered arginines is stabilized by one buried glutamate residue (Glu 58), which is strongly interacting with Arg 75 and Arg 38. This functional arrangement of three charged amino acid residues is of general significance because it is found in the constriction zones of all known 16-stranded porins from the alpha-, beta-, and gamma-proteobacteria.

Expression, two-dimensional crystallization, and three-dimensional reconstruction of the beta8 outer membrane protein Omp21 from Comamonas acidovorans.

The Omp21 protein from the proteobacterium Comamonas (Delftia) acidovorans belongs to the recently described beta8 family of outer membrane proteins, characterized by eight antiparallel beta-strands which form a beta-barrel. This family includes virulence proteins, OmpA and OmpX from Escherichia coli, and other related molecules. After we established an expression system, recombinant Omp21 was purified by Ni(2+) chelation affinity chromatography and refolded in situ while bound to resin. The native state of refolded protein was proven by FTIR spectroscopy and monitored with denaturing PAGE (heat modification). Both native and recombinant Omp21 were reconstituted in lipid membranes and crystallized two-dimensionally by controlled dialysis. Recombinant Omp21 crystallized as dimer and formed a p22(1)2(1) lattice with constants of a = 11.1 nm, b = 12.2 nm, gamma = 89.5 degrees. The 3-D structure of negatively stained, recombinant Omp21 was determined at a resolution of 1.8 nm by means of electron crystallography. Comparison with 3-D maps of OmpX and the transmembrane domain of OmpA revealed a high similarity between the mass distribution of exoplasmic loops of Omp21 and OmpA.

Factors affecting the freeze-fracture morphology of in vivo polyhydroxyalkanoate granules.

Interesting morphologies were observed when Comamonas acidovorans containing polyhydroxyalkanoates (PHA) of various compositions was freeze-fractured at temperatures far below the glass transition temperatures of PHA. In vivo granules of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) comparatively showed the most ductility, and could be stretched extensively. Contrary to the uniform needle-type deformation shown by the poly(3-hydroxybutyrate) homopolymer when fractured at -110 degrees C, copolymers containing 3-hydroxyvalerate units showed various deformation structures. Similar observations were made when in vivo granules of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) were freeze-fractured, although the ductility of the latter was much reduced. In addition, it was found that fracturing at -160 degrees C resulted in decreased ductility of the PHA granules with the concomitant increase in the number of mushroom-type deformation structures. Our results suggest that PHA granules with higher resistance to freeze-fracture deformation show less ductility, and therefore produce the mushroom-type morphology. This is the first report on the freeze-fracture morphology of PHA copolymers containing short-chain-length monomers.