A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria

This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.     

A proposed mechanism for the sol-gel transformation

The transformation from gel to sol in cell cytoplasm is treated as the transition from a lattice of macromolecules linked by Ca⁺⁺ ions to a random distribution of the macromolecules. The transition is a cooperative process, whose probability is expressed in terms of the theory of runs. The process is related to cell metabolism by the assumption that available Ca⁺⁺ concentration is regulated by metabolically produced endogenous chelating agents. Contribution 681 from the Division of Basic Health Sciences, Emory University.     

A proposed mechanism for multiplication of neural signals

The probability of the joint occurrence of two statistically independent events is the product of the probabilities of the individual events. This fact is used to show that a neuron which detects coincident arrivals of spikes from two input neurons can function as a multiplier, i.e. its average output spike frequency is proportional to the product of the average input spike frequencies. The theoretical analysis is checked in two ways: (a) Computer simulations confirm the derived expressions for the output frequency and show that increasing the jitter in the input spike trains improves the operation of the multiplier by making the output spike train more regular (b) Experimentally recorded spike trains are used to demonstrate that the type and amount of jitter present in real spike trains is adequate for satisfactory operation of the proposed scheme for multiplication. The operating characteristics of the proposed multiplier make it an attractive candidate for the multiplicative mechanism that is involved in the optomotor response of insects.     

The effect of hydraulic lift on organic matter decomposition,soil nitrogen cycling,and nitrogen acquisition by a grass species

Hydraulic lift (HL) is the passive movement of water through plant roots, driven by gradients in water potential. The greater soil–water availability resulting from HL may in principle lead to higher plant nutrient uptake, but the evidence for this hypothesis is not universally supported by current experiments. We grew a grass species common in North America in two-layer pots with three treatments: (1) the lower layer watered, the upper one unwatered (HL), (2) both layers watered (W), and (3) the lower layer watered, the upper one unwatered, but with continuous light 24 h a day to limit HL (no-HL). We inserted ingrowth cores filled with enriched-nitrogen organic matter (¹⁵N-OM) in the upper layer and tested whether decomposition, mineralization and uptake of ¹⁵N were higher in plants performing HL than in plants without HL. Soils in the upper layer were significantly wetter in the HL treatment than in the no-HL treatment. Decomposition rates were similar in the W and HL treatments and lower in no-HL. On average, the concentration of NH₄ ⁺-N in ingrowth cores was highest in the W treatment, and NO₃ ⁻-N concentrations were highest in the no-HL treatment, with HL having intermediate values for both, suggesting differential mineralization of organic N among treatments. Aboveground biomass, leaf ¹⁵N contents and the ¹⁵N uptake in aboveground tissues were higher in W and HL than in no-HL, indicating higher nutrient uptake and improved N status of plants performing HL. However, there were no differences in total root nitrogen content or ¹⁵N uptake by roots, indicating that HL affected plant allocation of acquired N to photosynthetic tissues. Our evidence for the role of HL in organic matter decomposition and nutrient cycling suggests that HL could have positive effects on plant nutrient dynamics and nutrient turnover.     

A phosphate transport system is required for symbiotic nitrogen fixation by Rhizobium meliloti.

The bacterium Rhizobium meliloti forms N2-fixing root nodules on alfalfa plants. The ndvF locus, located on the 1,700-kb pEXO megaplasmid of R. meliloti, is required for nodule invasion and N2 fixation. Here we report that ndvF contains four genes, phoCDET, which encode an ABC-type transport system for the uptake of Pi into the bacteria. The PhoC and PhoD proteins are homologous to the Escherichia coli phosphonate transport proteins PhnC and PhnD. The PhoT and PhoE proteins are homologous to each other and to the E. coli phosphonate transport protein PhnE. We show that the R. meliloti phoD and phoE genes are induced in response to phosphate starvation and that the phoC promoter contains two elements which are similar in sequence to the PHO boxes present in E. coli phosphate-regulated promoters. The R. meliloti ndvF mutants grow poorly at a phosphate concentration of 2 mM, and we hypothesize that their symbiotic phenotype results from their failure to grow during the nodule infection process. Presumably, the PhoCDET transport system is employed by the bacteria in the soil environment, where the concentration of available phosphate is normally 0.1 to 1 microM.     

A proposed role for inorganic carbon in water oxidation

This is an article on the peroxydicarbonic acid (PODCA) hypothesis of photosynthetic water oxidation, which follows our first article in this general area (Castelfranco et al., Photosynth Res 94:235–246, 2007). In this article I have expanded on the idea of a protein-bound intermediate containing inorganic carbon in some chemically bound form. PODCA is conceived in this article as constituting a bridge between two proteins of the oxygen-evolving complex (OEC) that are essential for the evolution of O₂. Presumably, these are two proteins which have been shown to possess Mn-dependent carbonic anhydrase activity (Lu et al., Plant Cell Physiol 46:1944–1953, 2005; Shitov et al., Biochemistry (Moscow) 74:509–517, 2009). One of these proteins may be the D_I of the OEC core and the other may be the PsbO extrinsic protein. I attempt to relate briefly the PODCA hypothesis to the role of two cofactors for O₂ evolution: Ca²⁺ and inorganic carbon. In this scheme, inorganic carbon (HCO₃ ^?) mediates the oxidation of peroxide to dioxygen, thus avoiding the homolytic cleavage of the peroxide into two free radicals. I visualize the role of Ca²⁺ in the binding of PODCA to two essential photosystem II proteins. I propose that PODCA alternates between two Phases. In Phase 1, PODCA is broken down with the production of O₂. In Phase 2, PODCA is regenerated.     

A proposed mechanism for the potentiation of cAMP-mediated acid secretion by carbachol

Acid secretion in isolated rabbit gastric glands was monitored by the accumulation of [(14)C]aminopyrine. Stimulation of the glands with carbachol synergistically augmented the response to dibutyryl cAMP. The augmentation persisted even after carbachol was washed out and was resistant to chelated extracellular Ca(2+) and to inhibitors of either protein kinase C or calmodulin kinase II. Cytochalasin D at 10 microM preferentially blocked the secretory effect of carbachol and its synergism with cAMP, whereas it had no effect on histamine- or cAMP-stimulated acid secretion within 15 min. Cytochalasin D inhibited the carbachol-stimulated intracellular Ca(2+) concentration ([Ca(2+)](i)) increase due to release from the Ca(2+) store. Treatment of the glands with cytochalasin D redistributed type 3 inositol 1,4,5-trisphosphate receptor (the major subtype in the parietal cell) from the fraction containing membranes of large size to the microsomal fraction, suggesting a dissociation of the store from the plasma membrane. These findings suggest that intracellular Ca(2+) release by cholinergic stimulation is critical for determining synergism with cAMP in parietal cell activation and that functional coupling between the Ca(2+) store and the receptor is maintained by actin microfilaments.     

On the mechanism and rate of substrate oxidation by amine oxidase from lentil seedlings

The kinetics of reaction between lentil seedlings amine oxidase and two amine substrates, namely putrescine and dimethylaminomethylbenzylamine, have been studied by rapid mixing with diode array detection. In this way several wavelengths can be monitored at once allowing the simultaneous measurement of enzyme bleaching and formation of a yellow radical intermediate. The two substrates are oxidized at rates that differ by one order of magnitude in favor of putrescine. Of the individual five rate constants measured and/or calculated from the experimental ones, k2 alone, the monomolecular transformation of ES to EP accounts for this difference. The reoxidation step is instead not rate limiting and identical for the two substrates.     

Growth and nitrogen acquisition strategies of Acacia senegal seedlings under exponential phosphorus additions

There remains conflicting evidence on the relationship between P supply and biological N₂-fixation rates, particularly N₂-fixing plant adaptive strategies under P limitation. This is important, as edaphic conditions inherent to many economically and ecologically important semi-arid leguminous tree species, such as Acacia senegal, are P deficient. Our research objective was to verify N acquisition strategies under phosphorus limitations using isotopic techniques. Acacia senegal var. senegal was cultivated in sand culture with three levels of exponentially supplied phosphorus [low (200 μmol of P seedling⁻¹ over 12 weeks), mid (400 μmol) and high (600 μmol)] to achieve steady-state nutrition over the growth period. Uniform additions of N were also supplied. Plant growth and nutrition were evaluated. Seedlings exhibited significantly greater total biomass under high P supply compared to low P supply. Both P and N content significantly increased with increasing P supply. Similarly, N derived from solution increased with elevated P availability. However, both the number of nodules and the N derived from atmosphere, determined by the ¹⁵N natural abundance method, did not increase along the P gradient. Phosphorus stimulated growth and increased mineral N uptake from solution without affecting the amount of N derived from the atmosphere. We conclude that, under non-limiting N conditions, A. senegal N acquisition strategies change with P supply, with less reliance on N₂-fixation when the rhizosphere achieves a sufficient N uptake zone.     

The mechanism of inhibition by EDTA and EGTA of methanol oxidation by methylotrophic bacteria

Ethyleneglycol (aminoethylether) tetra-acetic acid (EGTA) was shown to be a potent competitive inhibitor of electron transfer between methanol dehydrogenase (MDH) and its electron acceptor cytochrome cL. Addition of Ca2+ ions relieved the inhibition by removal of the inhibitory EGTA. Removal of EGTA by gel filtration completely relieved the inhibition. EGTA did not remove the tightly bound Ca2+ present in the MDH. Indo-1, a fluorescent analogue of EGTA, bound tightly to MDH in a 1:1 ratio but not to cytochrome cL; binding was prevented by EGTA. It was concluded that EGTA inhibits methanol oxidation by binding to lysyl or arginyl residues on MDH thus preventing docking with cytochrome cL.     

A proposed mechanism for the catalatic action of catalase

A detailed mechanism for catalatic action has been proposed which includes the formation of Chance's catalase compound I in the first step and hydride ion transfer in the second step. The first (oxidative) step involves direct reaction of hematin iron with an ionized H2O2 molecule, followed by an oxidation of the iron to Fe IV. The second step is assumed to depend upon the reductive action of a second H2O2 molecule on Chance's compound I through a catalyzed hybride ion transfer, resulting in the regeneration of uncomplexed catalase. Differences between the catalatic and peroxidative actions of catalase are discussed briefly in respect to the proposed mechanism for catalatic action. The rationale of the proposed mechanism is based to a considerable extent upon the type of ligand binding by the hematin iron of catalase, and this type of ligand bonding is contrasted with ligand binding in methemoglobin, which does not show catalatic activity. Finally, the dispositions of electrons in the outer electronic orbitals of the hematin iron of catalase and methemoglobin are discussed, as a means of justifying formulae presented for catalase and methemoglobin and their derivatives. One of the features of the proposed catalatic mechanism is the assumption, based on electron spin number, that the sixth coordination position around the hematin iron of uncomplexed catalase is unoccupied.     

Nitrogen acquisition by annual and perennial grass seedlings: testing the roles of performance and plasticity to explain plant invasion

Differences in resource acquisition between native and exotic plants is one hypothesis to explain invasive plant success. Mechanisms include greater resource acquisition rates and greater plasticity in resource acquisition by invasive exotic species compared to non-invasive natives. We assess the support for these mechanisms by comparing nitrate acquisition and growth of invasive annual and perennial grass seedlings in western North America. Two invasive exotic grasses (Bromus tectorum and Taeniatherum caput-medusae) and three perennial native and exotic grasses (Pseudoroegneria spicata, Elymus elymoides, and Agropyron cristatum) were grown at various temperatures typical of autumn and springtime when resource are abundant and dominance is determined by rapid growth and acquisition of resources. Bromus tectorum and perennial grasses had similar rates of nitrate acquisition at low temperature, but acquisition by B. tectorum significantly exceeded perennial grasses at higher temperature. Consequently, B. tectorum had the highest acquisition plasticity, showcasing its ability to take advantage of transient warm periods in autumn and spring. Nitrate acquisition by perennial grasses was limited either by root production or rate of acquisition per unit root mass, suggesting a trade-off between nutrient acquisition and allocation of growth to structural tissues. Our results indicate the importance of plasticity in resource acquisition when temperatures are warm such as following autumn emergence by B. tectorum. Highly flexible and opportunistic nitrate acquisition appears to be a mechanism whereby invasive annual grasses exploit soil nitrogen that perennials cannot use.     

Enhancement of symbiotic nitrogen fixation by vitamin-secreting fluorescent Pseudomonas

Fluorescent Pseudomonas sp. strain 267 promotes growth of nodulated clover plants under gnotobiotic conditions. In the growth conditions (60 M FeCl₃), the production of siderophores of the pseudobactin-pyoverdin group was repressed. Plant growth enhancement results from secretion of B vitamins by Pseudomonas sp. strain 267. This was proven by stimulation of clover growth by naturally auxotrophic strains of Rhizobium leguminosarum bv. trifolii and marker strains E. coli thi^- and R. meliloti pan^- in the presence of the supernatant of Pseudomonas sp. strain 267. The addition of vitamins to the plant medium increased symbiotic nitrogen fixation by the clover plants.     

A proposed mechanism for the lowering of mitochondrial electron leak by caloric restriction

Caloric restriction (CR) of laboratory rodents, which extends their maximum lifespan, only transiently reduces the specific metabolic rate of highly oxidative tissues. However, superoxide production by mitochondria of those tissues is greatly reduced by CR. This is probably a major contributor to the slowed aging seen in CR, but its mechanism is unknown. Here it is proposed that the major metabolic shift enabling reduced superoxide production is a diversion of much of the electron flux generated by glycolysis and the TCA cycle away from its usual destination, Complex I, and to the plasma membrane redox system. The cell's ATP synthesis capacity is thereby diminished, but so is its ATP demand, due to reduced turnover of the Na+/K+-ATPase. Direct tests of this hypothesis are proposed.     

The mechanism of ammonia assimilation in nitrogen fixing bacteria

Summary Enzymatic and genetic evidence are presented for a new pathway of ammonia assimilation in nitrogen fixing bacteria: ammonium glutamine glutamate. This route to the important glutamate-glutamine family of amino acids differs from the conventional pathway, ammonium glutamate glutamine, in several respects. Glutamate synthetase [(glutamine amide-2-oxoglutarate aminotransferase) (oxidoreductase)], which is clearly distinct from glutamate dehydrogenase, catalyzes the reduced pyridine nucleotide dependent amination of -ketoglutarate with glutamine as amino donor yielding two molecules of glutamate as product. The enzyme is completely inhibited by the glutamine analogue DON, whereas glutamate dehydrogenase is not affected by this inhibitor; the glutamate synthetase reaction is irreversible. Glutamate synthetase is widely distributed in bacteria; the pyridine nucleotide coenzyme specificity of the enzyme varies in many of these species.The activities of key enzymes are modulated by environmental nitrogenous sources; for example, extracts of N₂-grown cells of Klebsiella pneumoniae form glutamate almost exclusively by this new route and contain only trace amounts of glutamate dehydrogenase activity whereas NH₃-grown cells possess both pathways. Also, the biosynthetically active form of glutamine synthetase with a low K _m for ammonium predominates in the N₂-grown cell.Several mutant strains of K. pneumoniae have been isolated which fail to fix nitrogen or to grow in an ammonium limited environment. Extracts of these strains prepared from cells grown on higher levels of ammonium have low levels of glutamate synthetase activity and contain the biosynthetically inactive species of glutamine synthetase along with high levels of glutamate dehydrogenase. These mutants missing the new assimilatory pathway have serious defects in their metabolism of many inorganic and organic nitrogen sources; utilization of at least 20 different compounds is effected. We conclude that the new ammonia assimilatory route plays an important role in nitrogenous metabolism and is essential for nitrogen fixation.Abbreviation DON 6-diazo-5-oxo-l-norleucine     

A common pathway of sulfide oxidation by sulfate-reducing bacteria

Abstract Pseudomonas putida strain DMB capable of growing on 3,4-dimethylbenzoic acid as the only C and energy source was isolated by enrichment techniques. It does not utilize for growth or cooxidize the other dimethylbenzoate isomers tested. 3,4-Dimethylsalicylic acid, 3,4-dimethylphenol and 3,4-dimethylcatechol were isolated and identified by nuclear magnetic resonance and mass spectra in the reaction mixture of P. putida washed cells. The detection of the two first metabolites suggests that the initial step in the degradation of 3,4-dimethylbenzoic acid is the formation of 3,4-dimethylcyclohexa-3,5-diene-1, 2-diol-1-carboxylic acid which underwent an acid-catalyzed dehydration yielding 3,4-dimethylsalicylic acid and 3,4-dimethylphenol. Further degradation proceeds through 3,4-dimethylcatechol via the meta pathway.     

A proposed mechanism for myosin magnesium adenosine triphosphatase activity

A formal mechanism for the myosin MgATPase is proposed. The basic characteristics of this mechanism require that the binding of substrate at either one of two equivalent nucleotide sites of uncomplexed myosin prevents binding of substrate at the other unoccupied site (i.e. negative cooperativity) and that the rapid formation of a myosin-product complex permits binding of substrate at the unoccupied site. Analogue computer kinetic simulations indicate that the proposed mechanism is compatible with the observed transient phase kinetics characterizing the interaction of the enzyme with MgATP. In addition, analysis of the derived rate equation show that the mechanism is also consistent with existing steady-state kinetic data for the myosin MgATPase. A simpler mechanism is proposed for the subfragment-1 MgATPase that is shown to be compatible with the existing kinetic data. Features of the proposed myosin MgATPase mechanism are incorporated into a model of contraction which utilizes the bipartite structure and nucleotide site interaction of the myosin crossbridge to provide an efficient utilization of ATP in the contraction cycle.     

A proposed mechanism for light emission by bacterial luciferase involving dissociative electron transfer

A new mechanism that involves dissociative electron transfer in the energy transducing step is set forward for bacterial luciferase catalyzed light emission. The proposal involves (1) dissociation of the 4a-hydroperoxyflavin to a flavin radical and ${}^{\mathrm{?}}\text{O}{}_2{}^{\mathrm{?}}$, accounting for 570 and 620nm absorption, (2) ${}^{\mathrm{?}}\text{O}{}_2{}^{\mathrm{?}}$ addition to the aldehyde carbonyl to form a peroxyl radical, (3) abstraction of H from an enzyme thiol group to form RCH(OOH)OH, (4) thiyl radical abstraction of the H on C in RCH(OOH)OH, a step which can show a $\text{k}{}_{\mathrm{H}}\text{k}{}_{\mathrm{D}}$ of ca. 4, and (5) dissociative electron- transfer, a highly exothermic step that leads to a protonated flavin excited state, a carboxylic acid and water.