Electron microscope study of DNA-containing plasms. II. Vegetative and mature phage DNA as compared with normal bacterial nucleoids in different physiological states

The nucleoids of Escherichia coli, independently of the physiological state of the bacteria, are shown to be preserved as a fine-stranded fibrillar nucleoplasm by an OsO(4) fixation under defined conditions: acetate-veronal buffer pH 6, presence of Ca(++) and amino acids, stabilization with uranyl-acetate before dehydration. The same fixation procedure applied to the DNA of vegetative phage reveals a pool of homogeneous fibrillar structure very similar to the nucleoplasm. The "versene test," which produces a coarse coagulation of these plasms, emphasizes the similar behaviour of the pool and the nucleoids. The heads of mature phage are preserved in their true polyhedral shape by the standard fixation procedure, although they may be badly distorted when fixed under different conditions. Lanthanum nitrate and uranyl-acetate are shown to increase markedly the contrast of both phage and cytoplasm. The consequences of the fibrillar structure of the genetic material are discussed in relation to the probable division process.     

STUDIES ON THE FIXATION OF ARTIFICIAL AND BACTERIAL DNA PLASMS FOR THE ELECTRON MICROSCOPY OF THIN SECTIONS

The process of fixation of DNA-containing plasms is investigated by macroscopical and electron microscopical observations on solutions of DNA, nucleohistones, as well as on bacterial nuclei. The following treatments were found to produce a gelation of a solution of DNA or nucleohistones: (a) OsO₄ fixation at pH 6 in the presence of amino acids (tryptone) and Ca⁺⁺. (b) Exposure to aqueous solutions of uranyl acetate. (c) Exposure to aqueous solutions of indium chloride. Observed in the electron microscope, these gels show a fine fibrillar material. From experiments in which solutions of DNA or nucleohistones are mixed with bacteria and treated together, it is concluded that the behavior of the bacterial nucleoplasm is similar to that of the DNA solutions. The appearance of birefringence indicates that uranyl acetate and indium chloride produce an orientation of the molecules of a DNA solution during gelation. Bacterial chromosomes fixed by these agents also show a certain order, while those fixed by the OsO₄-amino acid-Ca⁺⁺ formula do not. Whether or not the order can be considered to be artificial is discussed, and a tentative conclusion is presented: (a) Uranyl acetate may induce artificial order. (b) Fixatives which do not gel DNA probably result in the grossest artifacts. (c) OsO₄ fixation at pH 6 in the presence of amino acids (tryptone) and Ca⁺⁺ may give the most accurate preservation of the in vivo disposition of DNA (RK⁺ fixation).     

PRESERVATION OF THE ULTRASTRUCTURE OF BACILLUS SUBTILIS BY CHEMICAL FIXATION AS VERIFIED BY FREEZE-ETCHING

The present study on the ultrastructure of Bacillus subtilis was undertaken in order to examine by means of the freeze-etching technique possible structural changes occurring during the chemical fixation procedure (Ryter-Kellenberger (R-K) fixation). Three stages were followed by freeze-etching, viz.: (a) fixation in osmium tetroxide, (b) fixation in osmium tetroxide and posttreatment with uranyl acetate, and (c) fixation in osmium tetroxide, posttreatment in uranyl acetate, and dehydration in a graded series of acetone. Preparations were made after each stage in the presence of 20% glycerol. Good preservation of ultrastructure was observed, after any of the three treatments, of the outer surface of the plasma membrane, and the inner surface of the plasma membrane. No alteration in fracturing properties could be observed. However, if we are to judge by the results of freeze-etching, any of the successive steps of the chemical fixation procedure achieve strong contrast between the nucleoplasmic region and the cytoplasm. Dependent on the quality of fixation, very delicately preserved DNA fibrils or strongly aggregated ones were seen. It appears that R-K fixation is capable of producing more or less distinctly visible changes in the native state of the nucleoplasm in young cells of B. subtilis.     

Extent and location of DNA synthesis associated with a class of Rec-mediated recombinants of bacteriophage lambda

The extent and location of DNA synthesis associated with Rec recombination of a lambda phage mutant has been determined approximately for recombinants arising under conditions that restrict DNA duplication. The mutant bio1 contains a substitution in its DNA, and nearly all phage maturing under these conditions have undergone a recombination event within a short region in or near the inserted DNA. Density labeled phage bio1 were used to prepare a lysate under these conditions and the extent of new DNA synthesis was determined by analyzing the density of the progeny phage. On the average, about 6% of the phage chromosome was resynthesized in such a cross.DNA was extracted from bio1 phage crossed under similar conditions in the presence of ³²PO₄. The position of incorporated ³²PO₄ was determined by cleaving the DNA with EcoRI restriction endonuclease and resolving the resulting fragments by electrophoresis on agarose gels. The fragment found to have the most newly synthesized DNA and the highest average amount of synthesis per nucleotide contains the bio1 insertion near its left end and the “hot spot” for Rec-mediated recombination near its center. It appears that in these crosses recombination-associated DNA synthesis is localized about the region of the Rec-mediated recombination event.     

Seasonal N2 fixation by cool-season pulses based on several15N methods

Summary Accurate estimates of N₂ fixation by legumes are requisite to determine their net contribution of fixed N₂ to the soil N pool. However, estimates of N₂ fixation derived with the traditional¹⁵N methods of isotope dilution and A_N value are costly.Field experiments utilizing¹⁵N-enriched (NH₄)₂SO₄ were conducted to evaluate a modified difference method for determining N₂ fixation by fababean, lentil, Alaska pea, Austrian winter pea, blue lupin and chickpea, and to quantify their net contribution of fixed N₂ to the soil N pool. Spring wheat and non-nodulated chickpea, each fertilized with two N rates, were utilized as non-fixing controls.Estimates of N₂ fixation based on the two control crops were similar. Increasing the N rate to the controls reduced A_N values 32, 18 and 43% respectively in 1981, 1982 and 1983 resulting in greater N₂ fixation estimates. Mean seasonal N₂ fixation by fababean, lentil and Austrian winter pea was near 80 kg N ha^–1, pea and blue lupin near 60 kg N ha^–1, and chickpea less than 10 kg N ha^–1. The net effects of the legume crops on the soil N pool ranged from a 70 kg N ha^–1 input by lentil in 1982, to a removal of 48 kg N ha^–1 by chickpea in 1983.Estimates of N₂ fixation obtained by the proposed modified difference method approximate those derived by the isotope dilution technique, are determined with less cost, and are more reliable than the total plant N procedure.Scientific paper No. 6605. College of Agriculture and Home Economics Research Center, Washington State University, Pullman, WA 99164, U.S.A.     

Differential effects of H2S on cytoplasmic and nuclear thiol concentrations in different tissues of Brassica roots

H₂S-fumigation experiments with the sulphur-demanding plant Brassica oleracea L. (hybrid curly kale) were carried out to modulate glutathione levels in root tip cells. Plants were exposed in small fumigation cabinets to 0.4 μl l^–1 H₂S for 96 h. The data obtained by HPLC analysis of bimane-labeled thiols showed a slight increase of glutathione contents of about 20% in the roots of H₂S fumigated plants. The histochemical non-destructive assay for the determination of glutathione in single cells of whole plant organs was carried out for the first time by the use of monochlorobimane (BmCl) in situ to give a fluorescent GSH–bimane conjugate, followed by a fixation procedure. A significant increase of the fluorescence signal after the H₂S treatment was localized in the cytoplasm as well as in the nucleoplasm of root meristem cells.     

Secretion of Extracellular Proteinases Active against Fibrillar Proteins by Micromycetes

It has been shown that micromycetes Aspergillus ustus 1 and Tolypocladium inflatum k1 secrete proteolytic enzymes that possess high collagenolytic, fibrinolytic, and elastolytic activity. The activity of proteinases hydrolyzing fibrillar proteins, which was determined by the cleavage of azo-collagen, was 122.6 × 10^–3E_Azc/mL in A. ustus 1 and 69.7 × 10^–3E_Azc/mL in T. inflatum k1 (E_Azc is the amount of azocollagen cleaved in 1 min (μg). The maximum values of activity were observed during submerged cultivation of A. ustus 1 for 4 days and of T. inflatum k1 for 5 days. It has been shown that the maximum of collagenolytic and general proteolytic activity during the cultivation of A. ustus 1 are time-separated, unlike T. inflatum k1, which, presumably, can simplify the procedure for obtaining proteinases active against fibrillar proteins.     

Intracellular events during infection by Haemophilus influenzae phage and transfection by its DNA

Intracellular events following infection of competent Haemophilus influenzae by HPlcl phage, or transfection by DNA from the phage, were examined. Physical separation of a large fraction of the intracellular phage DNA from the bulk of the host DNA was achieved by lysis of infected or transfected cells with digitonin, followed by low-speed centrifugation. The small amount of bacterial DNA remaining with the phage DNA in the supernatants could be distinguished from phage DNA by its ability to yield transformants. After infection by whole phage, three forms of intracellular phage DNA were observable by sedimentation velocity analysis: form III, the slowest-sedimenting one; form II, which sedimented 1.1 times faster than III, and form I, which sedimented 1.6 times faster than III. It was shown by electron microscopy, velocity sedimentation in alkali, and equilibrium sedimentation with ethidium bromide, that forms I, II and III are twisted circles, open circles, and linear duplexes, respectively.After the entry of phage DNA into wild-type cells in transfection, the DNA is degraded at early times, but later some of the fragments are reassembled, resulting in molecules that sediment faster than the monomer length of phage DNA. Some of the fast-sedimenting molecules are presumably concatemers and are generated by recombination. In strain rec₁^? the fast-sedimenting molecules do not appear and degradation of phage DNA is even more pronounced than in wild-type cells. In strain rec₂^? there is little degradation of phage DNA, and the proportion of fast-sedimenting molecules is much smaller than in wild-type cells. Since rec₁^? and rec₂^? are transfected with much lower efficiency than wild type, our hypothesis is that both fragmentation and generation of fast-sedimenting phage DNA by recombination are required for more efficient transfection.     

The Influence of Leaf Age on C(4) Photosynthesis and the Accumulation of Inorganic Carbon in Flaveria trinervia, a C(4) Dicot

Characteristics of C₄ photosynthesis were examined in young, mid-age, and mature leaves of Flaveria trinervia (an NADP-malic enzyme-type C₄ dicot). The turnover of [4-¹⁴C] (malate plus aspartate) following a pulse with ¹⁴CO₂ was similar in leaves of different ages (apparent half-time of 18-25 seconds). However, the rate of ¹⁴CO₂ incorporation in mid-age leaves was about 1.5-fold higher than in young leaves, and about 2.5-fold higher than in mature leaves. The rate of ¹⁴CO₂ fixation was proportional to the total active pool of malate plus aspartate but was not correlated with the total photosynthetically derived inorganic carbon pool. The leaf's ability to concentrate inorganic carbon photosynthetically declined during leaf expansion, from 29 down to 7 nanomoles per milligram chlorophyll. Similarly, the active aspartate pool also declined during leaf expansion, from about 123 down to 20 nanomoles per milligram chlorophyll. Enhanced metabolism of aspartate to CO₂ and pyruvate in young leaves is suggested to facilitate the maintenance of high CO₂ levels in bundle sheath cells which are thought to have a higher conductance to CO₂.     

Inactivation of transfecting DNA by physical and chemical agents: influence of genotypes of phage lambda and host cells

Inactivation of λ₁₁c and its purified DNA by UV irradiation, γ-rays of ¹³⁷Cs (in conditions of indirect action), nitrous acid, hydroxylamine and N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) was studied. The biological activity of isolated phage DNA was measured by the calcium transfection procedure. 14 different recipient strains of Escherichia coli K12 were used, including mutants deficient in excision and recombination repair (uvrA6, uvrB5, uvrC34, polA1, recA13, recC38, recD34, recA13B21C22, recA56uvrA6, exrA and recB21C22sbcB15).Whole phage was more resistant to the action of γ-rays than was isolated DNA. On the other hand, the chemical agents HNO₂ and MNNG inactivated phage much faster than isolated DNA. Of all mutations of the host cell only polA1 considerably increased the sensitivity of phage DNA to UV irradiation, γ-rays and MNNG. The mutations uvr^? affected the inactivation kinetics under UV action. In all other cases the genotype of the host cell was indifferent for the inactivation kinetics of phage DNA, even if it belonged to recombination deficient mutant λ red3 int6 (in which only UV and γ inactivation was studied). Possible reasons for the low efficiency of the host-cell repair toward the damage caused to λ DNA by different agents are discussed.     

THE GROWTH OF BACTERIOPHAGE

1. An anti-Escherichia coli phage has been isolated and its behavior studied. 2. A plaque counting method for this phage is described, and shown to give a number of plaques which is proportional to the phage concentration. The number of plaques is shown to be independent of agar concentration, temperature of plate incubation, and concentration of the suspension of plating bacteria. 3. The efficiency of plating, i.e. the probability of plaque formation by a phage particle, depends somewhat on the culture of bacteria used for plating, and averages around 0.4. 4. Methods are described to avoid the inactivation of phage by substances in the fresh lysates. 5. The growth of phage can be divided into three periods: adsorption of the phage on the bacterium, growth upon or within the bacterium (latent period), and the release of the phage (burst). 6. The rate of adsorption of phage was found to be proportional to the concentration of phage and to the concentration of bacteria. The rate constant k_a is 1.2 x 10^–9 cm.⁸/min. at 15°C. and 1.9 x 10^–9 cm.⁸/min. at 25°. 7. The average latent period varies with the temperature in the same way as the division period of the bacteria. 8. The latent period before a burst of individual infected bacteria varies under constant conditions between a minimal value and about twice this value. 9. The average latent period and the average burst size are neither increased nor decreased by a fourfold infection of the bacteria with phage. 10. The average burst size is independent of the temperature, and is about 60 phage particles per bacterium. 11. The individual bursts vary in size from a few particles to about 200. The same variability is found when the early bursts are measured separately, and when all the bursts are measured at a late time.     

SOS repair of 8-methoxypsoralene monoadducts in DNA of lambda bacteriophage and plasmids is mediated by MucA 2 ′ B, but not UmuD 2 ′ C (PolV) polymerase

The light-induced action of 8-methoxypsoralen (8-MOP) on λ phage and plasmids yields monoadducts and interstrand crosslinks. The survival and clear plaque mutation frequency in the phage photosensitized with 8-MOP and irradiated with UV at wavelength >320 nm are increased when the wild-type host (Escherichia coli uvr ⁺) is subjected to UV irradiation (wavelength = 254 nm) prior to phage inoculation. These phenomena are known as “W reactivation” and “W mutagenesis.” It is shown that 8-MOP monoadducts in λ DNA induce clear mutations in the phage inoculated to UV-irradiated excision repair mutants of E. coli only when the error-prone repair is performed by MucA ₂ ^′ B, but not PolV (UmuD ₂ ^′ C) polymerase. The efficiency of the SOS repair (W reactivation) of 8-MOP monoadducts in plasmid and λ phage DNA also only increases with the presence of pKM101 plasmid muc ⁺ in E. coli uvr ^?.     

A Model for HCO(3) Accumulation and Photosynthesis in the Cyanobacterium Synechococcus sp: Theoretical Predictions and Experimental Observations

A simple model based on HCO₃⁻ transport has been developed to relate photosynthesis and inorganic carbon fluxes for the marine cyanobacterium, Synechococcus sp. Nägeli (strain RRIMP N1). Predicted relationships between inorganic carbon transport, CO₂ fixation, internal carbonic anhydrase activity, and leakage of CO₂ out of the cell, allow comparisons to be made with experimentally obtained data. Measurements of inorganic carbon fluxes and internal inorganic carbon pool sizes in these cells were made by monitoring time-courses of CO₂ changes (using a mass spectrometer) during light/dark transients. At just saturating CO₂ conditions, total inorganic carbon transport did not exceed net CO₂ fixation by more than 30%. This indicates CO₂ leakage similar to that estimated for C₄ plants.

For this leakage rate, the model predicts the cell would need a conductance to CO₂ of around 10⁻⁵ centimeters per second. This is similar to estimates made for the same cells using inorganic carbon pool sizes and CO₂ efflux measurements. The model predicts that carbonic anhydrase is necessary internally to allow a sufficiently fast rate of CO₂ production to prevent a large accumulation of HCO₃⁻. Intact cells show light stimulated carbonic anhydrase activity when assayed using ¹⁸O-labeled CO₂ techniques. This is also supported by low but detectable levels of carbonic anhydrase activity in cell extracts, sufficient to meet the requirements of the model.

     

The Sensitivity of Moss-Associated Nitrogen Fixation towards Repeated Nitrogen Input

Nitrogen (N₂) fixation is a major source of available N in ecosystems that receive low amounts of atmospheric N deposition. In boreal forest and subarctic tundra, the feather moss Hylocomium splendens is colonized by N₂ fixing cyanobacteria that could contribute fundamentally to increase the N pool in these ecosystems. However, N₂ fixation in mosses is inhibited by N input. Although this has been shown previously, the ability of N₂ fixation to grow less sensitive towards repeated, increased N inputs remains unknown. Here, we tested if N₂ fixation in H. splendens can recover from increased N input depending on the N load (0, 5, 20, 80, 320 kg N ha^-1 yr^-1) after a period of N deprivation, and if sensitivity towards increased N input can decrease after repeated N additions. Nitrogen fixation in the moss was inhibited by the highest N addition, but was promoted by adding 5 kg N ha^-1 yr^-1, and increased in all treatments during a short period of N deprivation. The sensitivity of N₂ fixation towards repeated N additions seem to decrease in the 20 and 80 kg N additions, but increased in the highest N addition (320 kg N ha^-1 yr^-1). Recovery of N in leachate samples increased with increasing N loads, suggesting low retention capabilities of mosses if N input is above 5 kg N ha^-1 yr^-1. Our results demonstrate that the sensitivity towards repeated N additions is likely to decrease if N input does not exceed a certain threshold.     

Kinetics of hydrolysis of type I,II, and III collagens by the class I and IIClostridium histolyticum collagenases

The kinetics of hydrolysis of rat tendon type I, bovine nasal septum type II, and human placental type III collagens by class I and class IIClostridium histolyticum collagenases (CHC) have been investigated. To facilitate this study, radioassays developed previously for the hydrolysis of these [³H]acetylated collagens by tissue collagenases have been adapted for use with the CHC. While the CHC are known to make multiple scissions in these collagens, the assays are shown to monitor the initial proteolytic events. The individual kinetic parametersk _cat andK _M have been determined for the hydrolysis of all three collagens by both class I and class II CHC. The specific activities of these CHC toward fibrillar type I and III collagens have also been measured. In contrast to human tissue collagenases, neither class of CHC exhibits a marked specificity toward any collagen type either in solution or in fibrillar form. The values of the kinetic parametersk _cat andK _M for the CHC are similar in magnitude to those of the human enzymes acting on their preferred substrates. Thus, the widely held view that the CHC are more potent collagenases is not strictly correct. As with the tissue collagenases, the local collagen structure at the cleavage sites is believed to play an important role in determining the rates of the reactions studied.     

The action of mutagens on MS2 phage and on its infective RNA. V. Kinetics of the chemical and functional changes of the genome under hydroxylamine treatment

The kinetics of chemical and functional changes induced in the genome of bacteriophage MS2 by hydroxylamine under the conditions of predominant modification of either cytidine (pH 5.0) or uridine (pH 8.0) have been studied.Comparison of the kinetics of chemical modifications of monomeric nucleotides with those of bacteriophage inactivation at pH 8.0 and 5.0 made it possible to estimate the effective number of exposed cytidine and uridine residues in the intra-phage RNA (B_eff^c and B_eff^u). The B_eff^u was close to that expected and increased from 70 to 130 as the temperature rose from 0 to 30°. The B_eff^c was much greater than that expected on the basis of the results with the monomer, suggesting that side reactions are involved in the inactivation of the phage at pH 5.0.A significant increase of the frequency of mutation occurs only under the conditions of predominant modification of cytidine (pH 5.0) at 0°. No such effect was observed at 30°. This was probably due to the increased contribution of inactivating side reactions. The effect of hydroxylamine on the phage under the conditions of predominant uridine modification (pH 8.0) did not lead to an increase in frequency of mutants.Incubation of the intact phage in acetate buffer resulted in considerable inactivation and mutations. Inactivation was inhibited by magnesium ions. Incubation at pH 5.5, of the phage inactivated by hydroxylamine treatment at pH 8.0, resulted in a considerable increase of the inefectivity with no effect on the frequency of mutants. The infectivity and the mutation frequency of the phage treated with hydroxylamine at pH 5.0 did not change as a result of incubation at pH 4.0 after the removal of the reagent.     

Differential Expression of Uptake Hydrogenase Activity in Free Living Cells and Nodule Bacteroids of Azorhizobium caulinodans

An oxygen sensitive mutant of Azorhizobium caulinodans strain IRBG 46 in which N₂ fixation ability was affected, was previously isolated by NTG mutagenesis. Now, the mutation has been shown to affect H₂- uptake hydrogenase (Hup) activity under symbiotic conditions. However, free living Hup activity remained unaffected. Thus the mutant is Hup^- under symbiotic conditions and Hup⁺ under free living condtions. A possible regulatory link between N₂ fixation and H₂ uptake system has been discussed.     

Equilibration of metabolic CO2 with preformed CO2 and bicarbonate: An unexpected finding

Entry of metabolic ¹⁴CO₂ into urea is shown to occur more readily than it equilibrates with the general pool of cellular plus extracellular bicarbonate plus CO₂. Since the sites of CO₂ production (pyruvate dehydrogenase and oxoglutarate dehydrogenase) and of fixation (carbamoylphosphate synthetase) are intramitochondrial, it is likely that the fixation of CO₂ is also more rapid than its equilibration with the cytoplasmic pool of bicarbonate plus CO₂. This observation may point to a more general problem concerning the interpretation of isotope data, when compartmentation or proximity of sites of production and utilisation of metabolites may result in the isotope following a preferred pathway.