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Induction of the allantoin degradative enzymes in Saccharomyces cerevisiae by the last intermediate of the pathway.

Saccharomyces cerevisiae can degrade allantoin in five steps to glyoxylate, ammonia, and "CO(2)." We previously demonstrated that synthesis of the urea carboxylase-allophanate hydrolase multienzyme complex is contingent upon the presence of allophanic acid, the product of the urea carboxylase reaction. Since these enzymes catalyze the last two reactions of allantoin degradation, experiments were performed to establish whether or not the presence of allophanic acid was required for synthesis of any other enzymes participating in this degradative pathway. The data presented here indicate that allophanic acid is required for synthesis of all enzymes participating in allantoin degradation. This conclusion is based upon the observation that: (i) wild-type strains produced a large amount of allantoinase upon addition of allantoin, allantoate, ureidoglycolate, or urea to the medium, (ii) no increase in activity was observed unless the added compound could be metabolized to allophanate, (iii) strains lacking allophanate hydrolase contained large amounts of allantoinase even in the absence of added urea, and (iv) the urea analogue, formamide, was capable of inducing allantoinase synthesis in wild-type strains but would not serve this function in a strain lacking urea carboxylase.

Allantoin↗

Cell-free synthesis of adenovirus 2 proteins programmed by fractionated messenger RNA: a comparison of polypeptide products and messenger RNA lengths.

Cytoplasmic RNA extracted from human tissue culture cells infected with adenovirus type 2 was used to program protein synthesis in a cell-free system derived from mammalian cells. Analysis of the protein product by polyacrylamide gel electrophoresis revealed ten adenovirus-specific polypeptides. Five of these were further identified by analysis of tryptic peptides. Translation of RNA fractionated by sedimentation through sucrose gradients containing formamide demonstrated seven size classes of RNA, each of which programmed the synthesis of only one or two virus-specific polypeptides. Six of the virus-specific polypeptides were translated from RNAs much larger than expected for the size of the polypeptide.

Adenoviridae↗

Electronic distributions within protein phenylalanine aromatic rings are reflected by the three-dimensional oxygen atom environments.

The atomic environments of 170 phenylalanine-residue aromatic rings from 28 protein crystal structures are transformed into a common orientation and combined to calculate an average three-dimensional environment. The spatial distribution of atom types in this environment reveals a preferred interaction between oxygen atoms and the edge of the planar aromatic rings. From the difference in frequency of interaction of oxygen atoms with the edge and the top of the ring, an apparent net free energy difference of interaction favoring the edge of the ring is estimated to be about -1 kcal/mol (1 cal = 4.184 J). Ab initio quantum mechanical calculations, performed on a model consisting of benzene and formamide, indicate that the observed geometry is stabilized by a favorable enthalpic interaction. Although benzene rings are considered to be nonpolar, the electron distribution is a complex multipole with no net dipole moment. The observed interaction orientation frequencies demonstrate that these multipolar electron distributions, when occurring at the short distances encountered in densely packed protein molecules, are significant determinants of internal packing geometries.

Benzene↗

Surface tension measurements show that chaotropic salting-in denaturants are not just water-structure breakers.

Since the salting-in agents guanidinium chloride, urea, and lithium perchlorate increase the surface tension of water, the salting-in phenomenon does not reflect easier cavity formation in water. Therefore, these salting-in agents must be directly contributing to the solvation of a solute such as benzene in water, probably by a direct solvation interaction. The increased surface-tension effects do not overbalance these solvation effects since they are smaller than the large surface-tension increases with lithium chloride, a typical salting-out agent. The salting-in agent tetra-n-butylammonium chloride differs in that it lowers the surface tension of water. Thus, it probably contributes both to easier cavity formation and to direct solvation of the substrate. The previous findings that most salting-in agents switch to become salting-out agents in other polar solvents such as ethylene glycol and formamide but that tetra-n-butylammonium chloride does not switch in these solvents can be understood in terms of relative polarities.

Benzene↗

In vitro regulation of a SIN3-dependent DNA-binding activity by stimulatory and inhibitory factors.

The yeast SIN3 gene (also known as SDII, is a known negative regulator of the yeast HO gene. A DNA-binding activity, called SDP1, which binds to the HO promoter, is absent in extracts prepared from sin3 mutants and has been proposed to function as a repressor. We show that SIN3 does not encode SDP1 and that SDP1 DNA-binding activity is modulated in vitro by two factors, an inhibitory factor, I-SDP1, and a stimulatory factor, S-SDP1. I-SDP1 acts as an in vitro inhibitor of the SDP1 DNA-binding activity. Restoration of the DNA-binding activity is achieved by inclusion of a stimulatory factor, S-SDP1, which copurifies with the SIN3 protein. SDP1 DNA-binding activity was restored by treating a protein fraction containing SDP1 and I-SDP1 with the dissociating agent formamide.

Base Sequence↗

Characterization of lysine 56 of histone H3 as an acetylation site in Saccharomyces cerevisiae.

Post-translational histone modifications abound and regulate multiple nuclear processes. Most modifications are targeted to the amino-terminal domains of histones. Here we report the identification and characterization of acetylation of lysine 56 within the core domain of histone H3. In the crystal structure of the nucleosome, lysine 56 contacts DNA. Phenotypic analysis suggests that lysine 56 is critical for histone function and that it modulates formamide resistance, ultraviolet radiation sensitivity, and sensitivity to hydroxyurea. We show that the acetylated form of histone H3 lysine 56 (H3-K56) is present during interphase, metaphase, and S phase. Finally, reverse genetic analysis indicates that none of the known histone acetyltransferases is solely responsible for H3-K56 acetylation in Saccharomyces cerevisiae.

Alleles↗

Discovery of a novel enzyme, isonitrile hydratase, involved in nitrogen-carbon triple bond cleavage.

Isonitrile containing an N triple bond C triple bond was degraded by microorganism sp. N19-2, which was isolated from soil through a 2-month acclimatization culture in the presence of this compound. The isonitrile-degrading microorganism was identified as Pseudomonas putida. The microbial degradation was found to proceed through an enzymatic reaction, the isonitrile being hydrated to the corresponding N-substituted formamide. The enzyme, named isonitrile hydratase, was purified and characterized. The native enzyme had a molecular mass of about 59 kDa and consisted of two identical subunits. The enzyme stoichiometrically catalyzed the hydration of cyclohexyl isocyanide (an isonitrile) to N-cyclohexylformamide, but no formation of other compounds was detected. The apparent K(m) value for cyclohexyl isocyanide was 16.2 mm. Although the enzyme acted on various isonitriles, no nitriles or amides were accepted as substrates.

Carbon↗

Hydroxylation of deoxyguanosine at 5' site of GG and GGG sequences in double-stranded DNA induced by carbamoyl radicals.

Free radicals generated by chemicals can cause sequence-specific DNA damage and play important roles in mutagenesis and carcinogenesis. Carbamoyl group (CONH2) and its derived groups (CONR2) occur as natural products and synthetic chemical compounds. We have investigated the DNA damage by carbamoyl radicals .(CONH2), one of carbon-centered radicals. Electron spin resonance (ESR) spectroscopic study has demonstrated that carbamoyl radicals were generated from formamide by treatment with H2O2 plus Cu(II), and from azodicarbonamide by treatment with Cu(II). We have investigated sequence specificity of DNA damage induced by carbamoyl radicals using 32P-labeled DNA fragments obtained from the human c-Ha-ras-1 and p53 genes. Treatment of double-stranded DNA with carbamoyl radicals induced an alteration of guanine residues, and subsequent treatment with piperidine or Fpg protein led to chain cleavages at 5'-G of GG and GGG sequences. Carbamoyl radicals enhanced Cu(II)/H2O2-mediated formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) in double-stranded DNA more efficiently than that in single-stranded DNA. These results shows that carbamoyl radicals specifically induced hydroxylation of deoxyguanosine at 5' site of GG and GGG sequences in double-stranded DNA.

8-Hydroxy-2'-Deoxyguanosine↗

Effect of processing on Celecoxib and its solvates.

Pharmaceuticals mostly exist in crystalline form and exhibit the phenomenon of differential crystal packing and configurational arrangements of molecules, called polymorphism. Pharmaceutical processing by introducing significant amount of stress alters the molecular interactions in the system engendering polymorphic transformations. The energy supplied by these processing steps tends to overcome the energy barriers between different solid-state forms, thus yielding undesirable changes in the physicochemical and material characteristics of drugs or their dosage forms. Therefore, the role of these unit processes in solid-state transformations must be cautiously studied and if required appropriate controls should be used to monitor such events. The present study was aimed at studying the effect of major energy imparting pharmaceutical unit processes, like size reduction, wet granulation, consolidation, and compression on solid-state transformation of Celecoxib, a selective cyclooxygenase-II inhibitor and its N,N-dimethyl acetamide and N,N-dimethyl formamide solvated forms. A qualitative estimation of crystal transformation in processed samples was performed using DSC, microscopy, FTIR spectroscopy, and XRPD. FTIR was also applied for the development of a quantification method to find the percentage of transformation in N,N-dimethyl acetamide solvated form during compression.

Acetamides↗

Hybridization properties of DNA sequences directing the synthesis of messenger RNA and heterogeneous nuclear RNA.

The relationship of the DNA sequences from which polyribosomal messenger RNA (mRNA) and heterogeneous nuclear RNA (NRNA) of mouse L cells are transcribed was investigated by means of hybridization kinetics and thermal denaturation of the hybrids. Hybridization was performed in formamide solutions at DNA excess. Under these conditions most of the hybridizing mRNA and NRNA react at values of D(o)t (DNA concentration multiplied by time) expected for RNA transcribed from the nonrepeated or rarely repeated fraction of the genome. However, a fraction of both mRNA and NRNA hybridize at values of D(o)t about 10,000 times lower, and therefore must be transcribed from highly redundant DNA sequences. The fraction of NRNA hybridizing to highly repeated sequences is about 1.7 times greater than the corresponding fraction of mRNA. The hybrids formed by the rapidly reacting fractions of both NRNA and mRNA melt over a narrow temperature range with a midpoint about 11 degrees C below that of native L cell DNA. This indicates that these hybrids consist of partially complementary sequences with approximately 11% mismatching of bases. Hybrids formed by the slowly reacting fraction of NRNA melt within 4 degrees -6 degrees C of native DNA, indicating very little, if any, mismatching of bases. Hybrids of the slowly reacting components of mRNA, formed under conditions of sufficiently low RNA input, have a high thermal stability, similar to that observed for hybrids of the slowly reacting NRNA component. However, when higher inputs of mRNA are used, hybrids are formed which have a strikingly lower thermal stability. This observation can be explained by assuming that there is sufficient similarity among the relatively rare DNA sequences coding for mRNA so that under hybridization conditions, in which these DNA sequences are not truly in excess, reversible hybrids exhibiting a considerable amount of mispairing are formed. The fact that a comparable phenomenon has not been observed for NRNA may mean that there is less similarity among the relatively rare DNA sequences coding for NRNA than there is among the rare sequences coding for mRNA.

Animals↗

Structure of nuclear ribonucleoprotein: identification of proteins in contact with poly(A)+ heterogeneous nuclear RNA in living HeLa cells.

The processing of heterogeneous nuclear RNA into messenger RNA takes place in special nuclear ribonucleoprotein particles known as hnRNP. We report here the identification of proteins tightly complexed with poly(A)+ hnRNA in intact HeLa cells, as revealed by a novel in situ RNA-protein cross-linking technique. The set of cross-linked proteins includes the A, B, and C "core" hnRNP proteins, as well as the greater than 42,000 mol wt species previously identified in noncross-linked hnRNP. These proteins are shown to be cross-linked by virtue of remaining bound to the poly(A)+ hnRNA in the presence of 0.5% sodium dodecyl sulfate, 0.5 M NaCl, and 60% formamide, during subsequent oligo(dT)-cellulose chromatography, and in isopycnic banding in Cs2SO4 density gradients. These results establish that poly(A)+ hnRNA is in direct contact with a moderately complex set of nuclear proteins in vivo. This not only eliminates earlier models of hnRNP structure that were based upon the concept of a single protein component but also suggests that these proteins actively participate in modulating hnRNA structure and processing in the cell.

Centrifugation, Isopycnic↗

Role of leaflet asymmetry in the permeability of model biological membranes to protons, solutes, and gases.

Bilayer asymmetry in the apical membrane may be important to the barrier function exhibited by epithelia in the stomach, kidney, and bladder. Previously, we showed that reduced fluidity of a single bilayer leaflet reduced water permeability of the bilayer, and in this study we examine the effect of bilayer asymmetry on permeation of nonelectrolytes, gases, and protons. Bilayer asymmetry was induced in dipalmitoylphosphatidylcholine liposomes by rigidifying the outer leaflet with the rare earth metal, praseodymium (Pr3+). Rigidification was demonstrated by fluorescence anisotropy over a range of temperatures from 24 to 50 degrees C. Pr3+-treatment reduced membrane fluidity at temperatures above 40 degrees C (the phase-transition temperature). Increased fluidity exhibited by dipalmitoylphosphatidylcholine liposomes at 40 degrees C occurred at temperatures 1-3 degrees C higher in Pr3+-treated liposomes, and for both control and Pr3+-treated liposomes permeability coefficients were approximately two orders of magnitude higher at 48 degrees than at 24 degrees C. Reduced fluidity of one leaflet correlated with significantly reduced permeabilities to urea, glycerol, formamide, acetamide, and NH3. Proton permeability of dipalmitoylphosphatidylcholine liposomes was only fourfold higher at 48 degrees than at 24 degrees C, indicating a weak dependence on membrane fluidity, and this increase was abolished by Pr3+. CO2 permeability was unaffected by temperature. We conclude: (a) that decreasing membrane fluidity in a single leaflet is sufficient to reduce overall membrane permeability to solutes and NH3, suggesting that leaflets in a bilayer offer independent resistances to permeation, (b) bilayer asymmetry is a mechanism by which barrier epithelia can reduce permeability, and (c) CO(2) permeation through membranes occurs by a mechanism that is not dependent on fluidity.

Acetamides↗

Temperature dependence of nonelectrolyte permeation across red cell membranes.

The temperature dependence of permeation across human red cell membranes has been determined for a series of hydrophilic and lipophilic solutes, including urea and two methyl substituted derivatives, all the straight-chain amides from formamide through valeramide and the two isomers, isobutyramide and isovaleramide. The temperature coefficient for permeation by all the hydrophilic solutes is 12 kcal mol(-1) or less, whereas that for all the lipophilic solutes is 19 kcal mol(-1) or greater. This difference is consonant with the view that hydrophilic molecules cross the membrane by a path different from that taken by the lipophilic ones. The thermodynamic parameters associated with lipophile permeation have been studied in detail. DeltaG is negative for adsorption of lipophilic amides onto an oil-water interface, whereas it is positive for transfer of the polar head from the aqueous medium to bulk lipid solvent. Application of absolute reaction rate theory makes it possible to make a clear distinction between diffusion across the water-red cell membrane interface and diffusion within the membrane. Diffusion coefficients and apparent activation enthalpies and entropies have been computed for each process. Transfer of the polar head from the solvent into the interface is characterized by DeltaG(double dagger) = 0 kcal mol(-1) and DeltaS(double dagger) negative, whereas both of these parameters have large positive values for diffusion within the membrane. Diffusion within the membrane is similar to what is expected for diffusion through a highly associated viscous fluid.

Amides↗

Water and nonelectrolyte permeability of lipid bilayer membranes.

Both the permeability coefficients (Pd's) through lipid bilayer membranes of varying composition (lecithin [L], lecithin:cholesterol [LC], and spingomyelin:cholesterol [SC]) and the n-hexadecane:water partition coefficients (Knc's) of H2O and seven nonelectrolytes (1,6 hexanediol, 1,4 butanediol, n-butyramide, isobutyramide, acetamide, formamide, and urea) were measured. For a given membrane compositiin, Pd/DKnc (where D is the diffusion constant in water) is the same for most of the molecules tested. There is no extraordinary dependence of Pd on molecular weight; thus, given Pd(acetamide), Pd(1,6 hexanediol) is correctly predicted from the Knc and D values for the two molecules. The major exceptions are H2O, whose value of Pd/DKnc is about 10-fold larger, and urea, whose value is about 5-fold smaller than the general average. In a "tight" membrane such as SC, Pd(n-butyramide)/Pd(isobutyramide)=2.5; thus this bilayer manifests the same sort of discrimination between branched and straight chain molecules as occurs in many plasma membranes. Although the absolute values of the Pd's change by more than a factor of 100 in going from the tightest membrane (SC) to the loosest (L), the relative values remain approximately constant. The general conclusion of this study is that H2O and nonelectrolytes cross lipid bilayer membranes by a solubility-diffusion mechanism, and that the bilayer interior is much more like an oil (a la Overton) than a rubber-like polymer (a la Lieb and Stein).

Acetamides↗

Observations of some oxygen-containing and sulfur-containing organic molecules in cold dark clouds.

Observations of nine oxygen- and sulfur-containing organic molecules have been made toward the cold dark clouds TMC-1 and L134N. We have confirmed the presence of para-ketene (H2C2O) in TMC-1, have for the first time observed ortho-ketene, and find a total ketene column density approximately 1 x 10(13) cm-2. Thioformaldehyde (H2CS) is easily detectable in both TMC-1 and L134N, with a column density about 5 times larger in the former source (approximately 3 x 10(13) cm-2). The fractional abundance of ketene is comparable to the predictions of ion-molecule chemistry, while that of thioformaldehyde in TMC-1 is one to two orders of magnitude greater than that expected from such models at steady state. Interstellar sulfur chemistry thus continues to be poorly understood. We set upper limits for the column densities of formic acid (HCOOH), vinyl alcohol (CH2CHOH), methyl formate (HCO2CH3), formamide (NH2CHO), methyl mercaptan (CH3SH), isothiocyanic acid (HNCS), and thioketene (H2C2S) in both sources.

Astronomical Phenomena↗

The formamidase gene of Aspergillus nidulans: regulation by nitrogen metabolite repression and transcriptional interference by an overlapping upstream gene.

The ability to utilize formamide as a sole nitrogen source has been found in numerous fungi. We have cloned the fmdS gene encoding a formamidase from Aspergillus nidulans and found that it belongs to a highly conserved family of proteins separate from the major amidase families. The expression of fmdS is primarily regulated via AreA-mediated nitrogen metabolite repression and does not require the addition of exogenous inducer. Consistent with this, deletion analysis of the 5' region of fmdS has confirmed the presence of multiple AreA-binding sites containing a characteristic core GATA sequence. Under carbon starvation conditions the response to nitrogen starvation is eliminated, indicating that the lack of a carbon source may result in inactivation of AreA. Sequence analysis and isolation of cDNAs show that a gene of unknown function lies directly 5' of fmdS with its transcript overlapping the fmdS coding region. Disruption of the 5' gene and analysis of the effects of overexpression of this gene on fmdS expression has shown that expression of this upstream gene interferes with fmdS transcription, resulting in a strong dependence on AreA activation for expression. Therefore the relative position of these two genes is essential for normal regulation of fmdS.

Amidohydrolases↗

Role of Candida albicans in granulomatous tissue reactions. I. In vitro degradation of C. albicans and immunospecificity of split products.

Several mannan-containing fractions were obtained from whole cells, cell walls, and cytoplasm of Candida albicans by means of treatment with hot formamide or precipitation with (NH4)2SO4. The immunological and chemical characteristics of the fractions were compared with those of C. albicans mannan prepared by standard procedures. Antisera to C. albicans from rabbits immunized with whole cells of the organism were found to be primarily directed against the mannan content. With use of such antisera, mannan was localized in both the inner and outer layers of the cell wall, whereas the middle layer was found in all likelihood to represent the glucan polymer. Stepwise removal of mannan from whole cells or cell walls resulted in increasing loss of periodic acid-Schiff staining, immunofluorescence, and peroxidase reactivity. Thus, it appears that mannan is responsible for the ability of cell walls of C. albicans to be stained by periodic acid-Schiff or labeled with fluorescent antibody. The component of the pathogen most resistant to physical or chemical treatment was the glucan, which lacked all immunological reactivity.

Antigens, Fungal↗

Mung bean nuclease exhibits a generalized gene-excision activity upon purified Plasmodium falciparum genomic DNA.

A novel set of reaction conditions for mung bean nuclease has been described in which Plasmodium genes were specifically excised as intact fragments from purified DNA. We have now determined that under the new conditions mung bean nuclease cleaves precisely at sites outside of the coding region of every P. falciparum gene for which the extent of the protein coding region in genomic DNA is known. We conclude that this enzyme activity is probably a general one for P. falciparum genes. Introns are not specifically cleaved, although one gene contained a cleavage site within an intron. There is no direct relationship between dA.dT-richness and sites of cleavage under these conditions. Also contrary to the expectations of a model based on cleavage at denaturation bubbles, there was no general relationship between the concentration of the DNA denaturant, formamide, and the size of the resulting gene-containing fragments. Thus, the data strongly suggest the involvement of an altered DNA structure near gene boundaries in determining the recognition sites for this enzyme activity.

Animals↗