Sequence analysis and evolution of sea urchin (Lytechinus pictus and Strongylocentrotus purpuratus) histone H4 messenger RNAs

The putative histone H4 (F2a₁) mRNA has been isolated from early blastula Strongylocentrotus purpuratus sea urchin embryos. Nucleotide sequences of oligonucleotides obtained by digestion of this RNA with T₁ ribonuclease have been obtained and many are found to be colinear with the amino acid sequence of histone H4 protein. The sequences obtained from the H4 mRNAs of S. pnrpuratus have been compared with those obtained from Lytechinus pictus (Grunstein & Schedl, 1976). The two mRNAs for this highly conserved protein have undergone considerable divergence of the sort that would be predicted from the degeneracy of the genetic code. 11.5% of the bases have undergone substitution at a rate calculated to be 3 × 10^?9 base changes · codon^?1 · year^?1.     

F0F1 ATP synthase of Streptomycetes: Modulation of activity and oligomycin resistance by protein Ser/Thr kinases

Inverted membrane vesicles of Gram-positive actinobacteria Streptomyces fradiae, S. lividans, and S. avermitilis have been prepared and membrane-bound F₀F₁ ATP synthase has been biochemically characterized. It has been shown that the ATPase activity of membrane-bound F₀F₁ complex is Mg²⁺-dependent and moderately stimulated by high concentrations of Ca²⁺ ions (10–20 mM). The ATPase activity is inhibited by N,N′-dicyclohexylcarbodiimide and oligomycin A, typical F₀F₁ ATPase inhibitors that react with the membrane-bound F₀ complex. The assay of biochemical properties of the F₀F₁ ATPases of Streptomycetes in all cases showed the presence of ATPase populations highly susceptible and insensitive to oligomycin A. The in vitro labeling and inhibitory assay showed that the inverted phospholipid vesicles of S. fradiae contained active membrane-bound Ser/Thr protein kinase(s) phosphorylating the proteins of the F₀F₁ complex. Inhibition of phosphorylation leads to decrease of the ATPase activity and increase of its susceptibility to oligomycin. The in vivo assay confirmed the enhancement of actinobacteria cell sensitivity to oligomycin after inhibition of endogenous phosphorylation. The sequencing of the S. fradiae genes encoding oligomycin-binding A and C subunits of F₀F₁ ATP synthase revealed their close phylogenetic relation to the genes of S. lividans and S. avermitilis.     

Initial steps in the large-scale purification of Escherichia coli deoxyribonucleic acid-dependent ribonucleic acid polymerase

Histones from exponential and stationary-phase mouse L-cells were quantitated after acrylamide gel electrophoresis in order to investigate cell cycle-dependent changes in the mode of binding of the various fractions in chromatin. By introducing various concentrations of citrate and divalent cations in the medium used for cell lysis and isolation of nuclei prior to histone extraction it was possible to demonstrate that certain histone fractions are preferentially retained in either exponential or stationary-phase nuclei. Differential retention of lysine-rich F₁ was most evident when the lysing medium contained 1 mm Mg²⁺ and Ca²⁺ and 5 mm citrate (pH 2.75). In these conditions twice as much F₁ is retained in stationary as in exponential nuclei. Differential retention of arginine-rich histones was most evident when the lysing medium contained 10 mm Mg²⁺ and Ca²⁺ and no citrate. In these conditions more F_{2a 1} is retained in exponential than in stationary nuclei while the opposite is true for F₃. However, the total amount of arginine-rich fractions (F_{2a 1} + F₃) retained was found to be the same in both cell phases. The results are discussed in relation to known structural features of the histones.     

Isolation and characterization of a membrane-bound proteinase from rat liver.

The proteinase previously found in chromatin prepared from a total rat liver homogenate was purified from the rat liver mitochondrial fraction. The membrane-bound enzyme is solubilized in either 0.6% digitonin or 0.5 m phosphate buffer. After a 1330-fold purification, the enzyme appears homogeneous by acrylamide-gel electrophoresis. Sucrose density gradient centrifugation indicated a molecular weight of 22,500, a molecular weight of 23,500 ± 10% has been estimated by acrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The enzyme showed a high substrate specificity. Among several proteins tested, only glucagon, nonhistone chromosomal proteins, and histones are good substrates. A limited proteolysis was found for the very-lysine-rich histone H1, which was split into a high molecular weight fragment (M_r 13,000). The highly phosphorylated histone H1 isolated from regenerating rat liver 24 h after partial hepatectomy exhibited the same susceptibility to the proteinase as H1 from normal liver. Large polypeptides of a nonhistone chromosomal protein fraction were degraded more rapidly than the small ones. N-Acetyl-l-tyrosine ethyl ester was used with alcohol dehydrogenase and NAD in a coupled enzyme assay for the proteinase. The apparent Michaelis constant for the hydrolysis of N-acetyl-l-tyrosine ethyl ester is 5.0 × 10^?3m. The proteinase has catalytic properties simlar to trypsin and chymotrypsin. The pH optimum was around 8, soybean trypsin inhibitor depressed the enzymatic activity, and the serine modifying reagents diisopropyl phosphofluoridate and phenylmethanesulfonyl fluoride inactivated the enzyme. The affinity reagent for chymotrypsin-like active sites, l-1-tosylamido-2-phenylethyl chloromethyl ketone, inactivated the proteinase.     

Gas chromatographic measurement of urinary 5-fluoro-2'-deoxyuridine levels after barium salt precipitation and sephadex LH-20 cleanup

A fluorescent photoaffinity label—8-azido-1-N⁶-etheno-adenosine 5′-triphosphate (8-N₃ε ATP)—for ATP-binding proteins has been synthesized. The effectiveness of the label is demonstrated with F₁ATPase from Micrococcus luteus. 8-N₃ε ATP is a substrate for the enzyme in the presence of bivalent cations. Ultraviolet irradiation of F₁ATPase in the presence of the label and Mg²⁺ ions inhibits the enzyme irreversibly. The fluorescent label is bound preferentially to the β subunit of the enzyme. Labeling and inactivation are decreased by protection with ATP or ADP.     

Vertebrate cells lacking FEN-1 endonuclease are viable but hypersensitive to methylating agents and H2O2

The structure-specific FEN-1 endonuclease has been implicated in various cellular processes, including DNA replication, repair and recombination. In vertebrate cells, however, no in vivo evidence has been provided so far. Here, we knocked out the FEN-1 gene (FEN1) in the chicken DT40 cell line. Surprisingly, homozygous mutant (FEN1^–/–) cells were viable, indicating that FEN-1 is not essential for cell proliferation and thus for Okazaki fragment processing during DNA replication. However, compared with wild-type cells, FEN1^–/– cells exhibited a slow growth phenotype, probably due to a high rate of cell death. The mutant cells were hypersensitive to methylmethane sulfonate, N-methyl-N′-nitro-N-nitrosoguanidine and H₂O₂, but not to UV light, X-rays and etoposide, suggesting that FEN-1 functions in base excision repair in vertebrate cells.     

Influence of a specific histone kinase on the physico-chemical properties of chromatin In situ

The influence of a specific histone kinase, phosphorylating lysine-rich histone F₁, F_2a2, F_2b, on the physico-chemical properties of the chromatin in the whole undestroyed fixed cell, has been investigated.It was found that the exogenous histone kinase penetrates into the nuclei of the undestroyed fixed cells and into the isolated unfixed nuclei and changes the physico-chemical properties of the chromatin there, bringing about an increase in binding of a basic dye acridine orange and a decrease in its stability to heat.     

Establishment of Histone Modifications after Chromatin Assembly

Every cell has to duplicate its entire genome during S-phase of the cell cycle. After replication, the newly synthesized DNA is rapidly assembled into chromatin. The newly assembled chromatin ‘matures’ and adopts a variety of different conformations. This differential packaging of DNA plays an important role for the maintenance of gene expression patterns and has to be reliably copied in each cell division. Posttranslational histone modifications are prime candidates for the regulation of the chromatin structure. In order to understand the maintenance of chromatin structures, it is crucial to understand the replication of histone modification patterns. To study the kinetics of histone modifications in vivo, we have pulse-labeled synchronized cells with an isotopically labeled arginine (¹⁵N₄) that is 4 Da heavier than the naturally occurring ¹⁴N₄ isoform. As most of the histone synthesis is coupled with replication, the cells were arrested at the G1/S boundary, released into S-phase and simultaneously incubated in the medium containing heavy arginine, thus labeling all newly synthesized proteins. This method allows a comparison of modification patterns on parental versus newly deposited histones. Experiments using various pulse/chase times show that particular modifications have considerably different kinetics until they have acquired a modification pattern indistinguishable from the parental histones.     

The interaction of nucleotides with F1-ATPase inactivated with 4-chloro-7-nitrobenzofurazan

In common with the F₁-ATPase from other sources, yeast mitochondrial F₁-ATPase was inhibited by 4-chloro-7-nitrobenzofurazan. Total inhibition of the F₁-ATPase activity was compatible with the modification of a single tyrosine residue per F₁-ATPase molecule. Radioactive labelling experiments localized this modification on a β-subunit. The inactive modified enzyme retained the capacity to bind the photoaffinity label 8-azido-1,N⁶-etheno-ATP, which has previously been shown to bind nucleotide sites of low affinity. As well, the inactive modified enzyme bound MgATP with high affinity, yielding a K_d of 14 μM. The results are consistent with the hypothesis of alternating, or cooperative, site catalysis by F₁-ATPase.     

α and β subunits of F1-ATPase are required for survival of petite mutants in Saccharomyces cerevisiae

Although Saccharomyces cerevisiae can form petite mutants with deletions in mitochondrial DNA (mtDNA) (ρ^?) and can survive complete loss of the organellar genome (ρ^o), the genetic factor(s) that permit(s) survival of ρ^? and ρ^o mutants remain(s) unknown. In this report we show that a function associated with the F₁-ATPase, which is distinct from its role in energy transduction, is required for the petite-positive phenotype of S. cerevisiae. Inactivation of either the α or β subunit, but not the γ, δ, or ? subunit of F₁, renders cells petite-negative. The F₁ complex, or a subcomplex composed of the α and β subunits only, is essential for survival of ρ^o cells and those impaired in electron transport. The activity of F₁ that suppresses ρ^o lethality is independent of the membrane F_o complex, but is associated with an intrinsic ATPase activity. A further demonstration of the ability of F₁ subunits to suppress ρ^o lethality has been achieved by simultaneous expression of S. cerevisiae F₁α and γ subunit genes in Kluyveromyces lactis– which allows this petite-negative yeast to survive the loss of its mtDNA. Consequently, ATP1 and ATP2, in addition to the previously identified AAC2, YME1 and PEL1/PGS1 genes, are required for establishment of ρ^? or ρ^o mutations in S. cerevisiae.     

A first-principles bottom-up study of the magnetic interaction mechanism in the bulk ferromagnet p-O2N-C6F4-CNSSN

The crystals of the p-nitro perfluorophenyl dithiadiazolyl radical have been shown to present bulk ferromagnetism below 1.32 K. Using our first-principles bottom-up methodology, the mechanism of the magnetic interactions in these crystals has been studied to gain a rigorous quantitative understanding of such bulk ferromagnetism. The p-O₂N-C₆F₄-CNSSN crystal is found to present only two non-negligible interactions (J(d1) = 0.83 cm^?1 and J(d3) = 0.07 cm^?1). The dominant interaction J(d1) generates a three-dimensional (3D) magnetic topology that can be described as a distorted diamond-like arrangement. Using the appropriate minimal magnetic model to describe this topology, the magnetic susceptibility and heat capacity curves were computed. A good agreement is found between the computed and experimental magnetic susceptibility data. Furthermore, the critical temperature obtained from the heat capacity curve (0.6 K) agrees well with the experimental one. A comparison of the magnetic data for p-O₂N-C₆F₄-CNSSN and four nitronyl nitroxide bulk ferromagnets indicates that the critical temperature not only depends on the size of the largest J interactions, but also on the corresponding magnetic topology.     

Evidence for Involvement of Gut-Associated Denitrifying Bacteria in Emission of Nitrous Oxide (N2O) by Earthworms Obtained from Garden and Forest Soils

Earthworms (Aporrectodea caliginosa, Lumbricus rubellus, and Octolasion lacteum) obtained from nitrous oxide (N₂O)-emitting garden soils emitted 0.14 to 0.87 nmol of N₂O h⁻¹ g (fresh weight)⁻¹ under in vivo conditions. L. rubellus obtained from N₂O-emitting forest soil also emitted N₂O, which confirmed previous observations (G. R. Karsten and H. L. Drake, Appl. Environ. Microbiol. 63:1878–1882, 1997). In contrast, commercially obtained Lumbricus terrestris did not emit N₂O; however, such worms emitted N₂O when they were fed (i.e., preincubated in) garden soils. A. caliginosa, L. rubellus, and O. lacteum substantially increased the rates of N₂O emission of garden soil columns and microcosms. Extrapolation of the data to in situ conditions indicated that N₂O emission by earthworms accounted for approximately 33% of the N₂O emitted by garden soils. In vivo emission of N₂O by earthworms obtained from both garden and forest soils was greatly stimulated when worms were moistened with sterile solutions of nitrate or nitrite; in contrast, ammonium did not stimulate in vivo emission of N₂O. In the presence of nitrate, acetylene increased the N₂O emission rates of earthworms; in contrast, in the presence of nitrite, acetylene had little or no effect on emission of N₂O. In vivo emission of N₂O decreased by 80% when earthworms were preincubated in soil supplemented with streptomycin and tetracycline. On a fresh weight basis, the rates of N₂O emission of dissected earthworm gut sections were substantially higher than the rates of N₂O emission of dissected worms lacking gut sections, indicating that N₂O production occurred in the gut rather than on the worm surface. In contrast to living earthworms and gut sections that produced N₂O under oxic conditions (i.e., in the presence of air), fresh casts (feces) from N₂O-emitting earthworms produced N₂O only under anoxic conditions. Collectively, these results indicate that gut-associated denitrifying bacteria are responsible for the in vivo emission of N₂O by earthworms and contribute to the N₂O that is emitted from certain terrestrial ecosystems.     

Function of coenzyme F420-dependent NADP reductase in methanogenic archaea containing an NADP-dependent alcohol dehydrogenase

Methanogenic archaea growing on ethanol or isopropanol as the electron donor for CO₂ reduction to CH₄ contain either an NADP-dependent or a coenzyme F₄₂₀-dependent alcohol dehydrogenase. We report here that in both groups of methanogens, the N ⁵, N ¹⁰-methylenetetrahydromethanopterin dehydrogenase and the N ⁵, N ¹⁰-methylenetetrahydromethanopterin reductase, two enzymes involved in CO₂ reduction to CH₄, are specific for F₄₂₀. This raised the question how F₄₂₀H₂ is regenerated in the methanogens with an NADP-dependent alcohol dehydrogenase. We found that these organisms contain catabolic activities of an enzyme catalyzing the reduction of F₄₂₀ with NADPH. The F₄₂₀-dependent NADP reductase from Methanogenium organophilum was purified and characterized. The N-terminal amino acid sequence showed 42% sequence identity to a putative gene product in Methanococcus jannaschii, the total genome of which has recently been sequenced. Received: 12 May 1997 / Accepted: 1 July 1997     

The extent of mitochondrial F1-ATPase and adenine nucleotide carrier activity with ϵ-ATP

1. The use of 1,N⁶-ethenoadenosine 5′-triphosphate (?-ATP), a synthetic, fluorescent analog of ATP, by whole rat liver mitochondria and by submitochondrial particles produced via sonication has been studied.2. Direct [³H]adenine nucleotide uptake studies with isolated mitochondria, indicate the ?-[³H]ATP is not transported through the inner membrane by the adenine nucleotide carrier and is therefore not utilized by the 2,4-dinitrophenol-sensitive F₁-ATPase (EC 3.6.1.3) that functions in oxidative phosphorylation. However, ?-ATP is hydrolyzed by a Mg²⁺-dependent, 2,4-dinitrophenol-insensitive ATPase that is characteristic of damaged mitochondria.3. ?-ATP can be utilized quite well by the exposed F₁-ATPase of sonic submitochondrial particles. This ?-ATP hydrolysis activity is inhibited by oligomycin and stimulated by 2,4-dinitrophenol. The particle F₁-ATPase displays similar K_m values for both ATP and ?-ATP; however, the V with ATP is approximately six times greater than with ?-ATP.4. Since ?-ATP is a capable substrate for the submitochondrial particle F₁-ATPase, it is proposed that the fluorescent properties of this ATP analog might be employed to study the submitochondrial particle F₁-ATPase complex, and its response to various modifiers of oxidative phosphorylation.     

Ozone sensitivity of four Pakchoi cultivars with different leaf colors: physiological and biochemical mechanisms

Ozone (O₃) is important air pollutant inducing severe losses of horticultural production. Cultivars of the same species, but with different leaf colors, may differ in their ozone sensitivity. However, it has not been clarified yet if different leaf coloration influences such a sensitivity. In this study, two purple-leafed and two green-leafed cultivars of Pakchoi were selected for ozone fumigation (240 ± 20 nmol mol^–1, 09:00–16:00 h). Elevated O₃ decreased chlorophyll content, increased anthocyanin (Ant) content, damaged cell membrane integrity, enhanced antioxidative enzyme activities, depressed photosynthetic rate (P _N) and stomatal conductance (g _s), inhibited maximal quantum yield (F_v/F_m) and effective quantum yield [Y_II] of PSII photochemistry, and caused visible injury. Purple-leafed cultivars with higher Ant contents were more tolerant than green-leafed cultivars as indicated by lower relative enhancement in malondialdehyde content and lower relative losses in P _N, g _s, F_v/F_m, and Y_II. The higher ability to synthesize Ant in the purple-leafed cultivars contributed to their higher photoprotective ability.     

Measurement of the overall volumetric coefficient of heat transfer of a shaking flask

The overall volumetric coefficient of heat transfer (Ua) of a shaking flask was measured under various shaking conditions using three types of flask. Ua was significantly affected by flask weight (W_F), which could be attributed to the thickness of the flask wall, the rotational speed of the shaker (N), wind velocity (V_W), and the liquid volume in the flask (V_L). The limiting step of heat transfer seemed to be the heat radiation process from the surface of the flask to the surroundings. To predict the value of Ua, the following empirical equations were obtained for each type of flask by the least squares method:

• 1.(1) for deformed creased flask (M-type flask), Ua=17.4 W_F^−0.43V_L^−0.61N^0.12V_W^0.36
• 2.(2) for creased flask (N-type flask), Ua=9.2 W_F^−0.36V_L^−0.57N^0.17V_W^0.27
• 3.(3) for smooth flask (S-type flask), Ua=5.3 W_F^−0.26V_L^−0.62N^0.19V_W^0.25.

     

FURTHER CHARACTERIZATION OF THE F1-HISTONE PHOSPHOKINASE OF METAPHASE-ARRESTED ANIMAL CELLS

Exponentially growing Chinese hamster cells are found to contain two major phosphokinase activities with specificity for the phosphorylation of F1 (lysine-rich) histone. These two activities, designated KI and KII, were extracted with 0.35 M NaCl and fractionated in 0.2 M NaCl by Sephadex G-200 gel filtration. KI, which is similar to the ubiquitous cyclic 3',5'-adenosine monophosphate (cAMP)-dependent phosphokinase, differs from KII by several criteria. KII is mol wt 90,000, cAMP independent, rapidly turned over in vivo, low K_m for ATP, and phosphorylates F1 histone at several unique sites. Comparative examination of metaphase-arrested (M) and counterpart interphase (I) cells for these two activities reveals that KII is responsible for the overall high activity in M-arrested cells. Pulse labeling of cells with ³²P during traverse of the G₂-M phase of the cell cycle reveals an in vivo tryptic-phosphopeptide pattern in whole unfractionated F1 which is unique to M cells. Seven major phosphopeptides derived by in vitro phosphorylation of F1 with the KII enzyme correspond to these M cell-specific phosphorylation sites observed in vivo. It is suggested that KII activity predominates during the G₂-M transition and that F1 is its natural in vivo substrate.     

Further purification of bovine spleen inhibitors of lymphocyte DNA synthesis (chalones)

Partially purified lymphocytic factors were obtained from bovine spleen; these factors are non-cytotoxic and biologically active in vitro and in vivo:[³H]Thymidine incorporation into DNA of mitogen-stimulated mouse spleen cells in culture is inhibited: similar results are obtained with phytohaemagglutinin-stimulated peripheral human lymphocytes, where blast cells transformation is blocked.[³H]Thymidine incorporation into DNA of mitogen stimulated lymphocytes withdrawn from in vivo treated mice, is also reduced.The two factors in vitro and in vivo seem to act preferentially on mouse spleen cells compared to their action on liver, kidney and testicle cells in culture as far as thymidine incorporation into DNA is concerned.The following techniques were applied for their purification: 1. Homogenization of the fresh tissue in water, centrifugation, dialysis of the supernatant, centrifugation fractionation of the supernatant by alcoholic precipitation and finally concentration in vacuo and lyophilization of the material soluble at 75% of alcohol yielded fraction F. 2. Preparation of an acetone powder from the spleen, extraction of the dry powder with water, then high speed centrifugation, followed by lyophilization of the supernatant produced fraction F′.Both fractions F and F′ were further fractioned by chromatography on a Sephadex G75 column: 7 peaks were obtained (F₁–F₇). Biological activity was found in fraction F₁, corresponding to high molecular weight material, and in fraction F₁, corresponding to low molecular weight substances.By rechromatography on Sephadex G 75, it is easy to dissociate from F₁ a small molecular weight fraction which might be similar to F₆ as far as elution volume and biological properties are concerned.