bluuebunny/crossref_metadata_2025 huggingface dataset:
Polypeptide-dependent protein kinase from bakers' yeast.
Authors: Yanagita Y , Abdel-Ghany M , Raden D , Nelson N , Racker E
Published: May 2006

The purification and properties of a protein serine kinase (PK-P) extracted with Triton X-100 from membranes of bakers' yeast are described. The enzyme is virtually inactive unless either a histone or a heat-stable polypeptide from yeast membranes and Mg2+ are added. Other divalent cations substitute for Mg2+ poorly or not at all; most of them, including Mn2+, inhibit when added in the presence of 5 mM Mg2+. The enzyme is unstable but can be stabilized by addition of 0.1% Triton X-100 and 20% glycerol. The final preparation shows, on silver-stained electrophoresis gels, two major bands (Mr 41,000 and 35,000). According to gel filtration the molecular weight of the active protein is about 75,000. Of the two subunits, only the smaller one appears to be autophosphorylated. In addition to casein, the enzyme phosphorylates several proteins including the H+-ATPase (Mr 100,000) in the yeast plasma membrane. In order to demonstrate the phosphorylation of the ATPase (up to 0.9 equivalents), exposure of the latter to an acid phosphatase was required. Other phosphorylated proteins include mRNA cap-binding protein from mammalian erythrocytes and yeast, a glucocorticoid receptor protein, and a preparation of the guanine nucleotide-binding proteins Gi and Go from brain. A partial purification of a natural activator from yeast plasma membranes is described.
Designing substrate specificity by protein engineering of electrostatic interactions.
Authors: Wells J A , Powers D B , Bott R R , Graycar T P , Estell D A
Published: May 2006

Protein engineering of electrostatic interactions between charged substrates and complementary charged amino acids, at two different sites in the substrate binding cleft of the protease subtilisin BPN', increases kcat/Km toward complementary charged substrates (up to 1900 times) and decreases kcat/Km toward similarly charged substrates. From kinetic analysis of 16 mutants of subtilisin and the wild type, the average free energies for enzyme-substrate ion-pair interactions at the two different sites are calculated to be -1.8 +/- 0.5 and -2.3 +/- 0.6 kcal/mol (1 cal = 4.18 J) [at 25 degrees C in 0.1 M Tris X HCl (pH 8.6)]. The combined electrostatic effects are roughly additive. These studies demonstrate the feasibility for rational design of charged ligand binding sites in proteins by tailoring of electrostatic interactions.
Mechanism of carboxypeptidase A: hydration of a ketonic substrate analogue.
Authors: Christianson D W , David P R , Lipscomb W N
Published: May 2006

The structure of the complex between carboxypeptidase A alpha (EC 3.4.17.1) and the ketonic substrate analogue 5-benzamido-2-benzyl-4-oxopentanoic acid (BOP) has been determined by x-ray crystallographic methods to a resolution of 1.7 A (final R = 0.191). Interestingly, BOP was observed to bind to the active site of carboxypeptidase A alpha as the covalent hydrate adduct. Because BOP is probably less than 0.2% hydrated in aqueous solution, this result was unexpected. One possibility is that the zinc-bound water of the native enzyme added to the ketone carbonyl. Alternatively, the enzyme may preferentially scavenge the hydrated ketone as it is continuously maintained at equilibrium in the solution in which the carboxypeptidase A alpha crystals were immersed. In either case, this mode of binding of BOP to carboxypeptidase A alpha provides an example of the preferred binding of a model of a structure along the reaction coordinate of a hydrolytic reaction.
Inhibition of glycolate and D-lactate metabolism in a
Chlamydomonas reinhardtii
mutant deficient in mitochondrial respiration
Authors: Husic Diane W. , Tolbert N. E.
Published: May 2006

The possibility that glycolate oxidation in unicellular green algae is linked to mitochondrial electron transport, rather than to peroxisomal metabolism as in higher plants and animals, was studied in a mutant of
Chlamydomonas reinhardtii
(dk97) deficient in cytochrome oxidase. This mutant had normal rates of dark respiration (40 ± 15 μmol of O
2
uptake per hr per mg of chlorophyll) but had only 11% of wild-type levels of cytochrome oxidase activity. Salicylhydroxamic acid (SHAM) reduced the dark respiration rate of dk97 cells by 71%, but cyanide did not significantly inhibit this rate. During photosynthesis in the presence of SHAM, glycolate oxidation was blocked, resulting in glycolate accumulation and excretion by mutant cells but not by wild-type
Chlamydomonas
. D-Lactate, which accumulated after brief periods of anaerobiosis in
Chlamydomonas
, was reoxidized by air-grown cells only aerobically in the light, and reoxidation of D-lactate was blocked by SHAM in the dk97 cells. Thus, glycolate and D-lactate dehydrogenase activities are both linked to mitochondrial electron transport in
Chlamydomonas
. During photosynthetic
14
CO
2
fixation by dk97 cells in the presence of SHAM,
14
C-labeled tricarboxylic acid cycle intermediates accumulated, indicating that, in
Chlamydomonas
, mitochondrial respiration functions during photosynthesis.
Detailed ordering of markers localizing to the Xq26-Xqter region of the human X chromosome by the use of an interspecific Mus spretus mouse cross.
Authors: Avner P , Amar L , Arnaud D , Hanauer A , Cambrou J
Published: May 2006

Five probes localizing to the Xq26-Xqter region of the human X chromosome have been genetically mapped on the mouse X chromosome using an interspecific cross involving Mus spretus to a contiguous region lying proximally to the Tabby (Ta) locus. Pedigree and recombinational analysis establish the marker order as being Hprt-FIX-c11-G6PD-St14-1. The size of this contiguous region is such that the X-linked muscular dystrophy (mdx) mouse mutation probably maps within this segment. This in turn suggests that it is highly improbable that the mouse mdx locus represents a model for Duchenne muscular dystrophy (DMD). It is, however, compatible with the idea that this mutation may correspond in man to Emery Dreifuss muscular dystrophy. The high frequency of restriction fragment length polymorphisms found in this interspecific system for all the human cross-reacting probes examined up until now, using only a limited number of restriction enzymes, suggests that the Mus spretus mapping system may be of great potential value for establishing the linkage relationships existing in man when conserved chromosomal regions are concerned and human/mouse cross-reacting probes are available or can be obtained.
Regulation by cell metabolism and adenine nucleotides of a K channel in insulin-secreting B cells (RIN m5F).
Authors: Ribalet B , Ciani S
Published: May 2006

A potassium channel in membranes of the insulin-secreting B-cell line, RIN m5F, was studied using the patch-clamp technique. In cell-attached patches, and for pipette solutions containing 140 mM KCl, the I-V curves exhibited a pronounced rectification, with the conductance being higher when the current flowed from the electrode into the cell (50 pS). Addition of glucose (5-7 mM) to the bath was sufficient to abolish the channel activity, while low doses of the metabolic inhibitor 2,4-dinitrophenyl enhanced it, indicating a link between channel activity and cell metabolism. In excised inside-out patches, the activity of a channel with similar conductive properties was inhibited by ATP in a dose-dependent fashion, the half-maximal concentration being approximately 70 microM. ADP also acted as an inhibitor, but with much lower potency. However, when ADP was present, the blocking effectiveness of ATP was reduced, suggesting a nonadditive interaction of the two nucleotides with the channel. In conclusion, complete closure of the K channel by glucose (5-7 mM) suggests that this channel may be responsible for the early phase of the B-cell depolarization, which is seen in normal cells for glucose increments up to similar values. In addition, since ATP and ADP are both present in the cells, the reduction by ADP of the blocking efficacy of ATP in excised patches may help one to understand why, in intact cells, the channel is still functional for intracellular ATP concentrations that in excised patches would completely suppress its activity.
Multicopy plasmid with a structure related to the polyoma virus genome.
Authors: Kusano T , Uehara H , Saito H , Segawa K , Oishi M
Published: May 2006

In a subclone derived from mouse L(tk-) cells, we found a plasmid present in a high copy number (greater than 5000 copies per cell) that was stably maintained extrachromosomally without any cytopathic effect to the host cells. This plasmid, termed L factor, has two forms: 5.3 and 5.5 kilobase pairs. DNA sequencing and restriction enzyme mapping showed that, although the structure contains DNA sequences common to polyoma virus, plasmid sequences belonging to the regulatory region (the enhancer region) and other regions are quite different from those in polyoma. In cells bearing the plasmid, we detected a low level of material that cross-reacts with antibody to polyoma tumor antigens, suggesting that the plasmids replicate and are maintained in the cells by a mechanism different from that functioning during propagation following infection of papovaviruses.
Cauliflower mosaic virus coat protein is phosphorylated
in vitro
by a virion-associated protein kinase
Authors: Martinez-Izquierdo José , Hohn Thomas
Published: May 2006

A protein kinase has been found to be associated with particles of the plant virus cauliflower mosaic virus. This protein kinase can phosphorylate endogenous viral capsid proteins
in vitro
and exchange substrates with casein kinase type II. The activity is not affected by cAMP but is enhanced considerably by ADP. The cofactor is either Mn
2+
or Mg
2+
, and the phosphate donor is either ATP or GTP. Serine and threonine residues are phosphorylated.
A major factor contributing to epidermal proliferation in inflammatory skin diseases appears to be interleukin 1 or a related protein.
Authors: Ristow H J
Published: May 2006

Human peripheral blood leukocytes can stimulate G1(G0)-arrested mouse skin keratinocytes to enter the cell cycle again and synthesize DNA at the maximum rate 15-20 hr later. This growth-promoting activity is released by the monocyte fraction and is shown to have characteristics that have been reported for interleukin 1 (IL-1). Pure IL-1 is active in stimulating keratinocyte cultures as was shown with recombinant human IL-1. An IL-1-like protein released by monocytes-macrophages could explain the hyperproliferative epidermis found in certain types of inflammatory skin diseases.
Cloning and characterization of cDNAs encoding the complete sequence of decay-accelerating factor of human complement.
Authors: Medof M E , Lublin D M , Holers V M , Ayers D J , Getty R R , Leykam J F , Atkinson J P , Tykocinski M L
Published: May 2006

cDNAs encoding the complement decay-accelerating factor (DAF) were isolated from HeLa and differentiated HL-60 lambda gt cDNA libraries by screening with a codon preference oligonucleotide corresponding to DAF NH2-terminal amino acids 3-14. The composite cDNA sequence showed a 347-amino acid protein preceded by an NH2-terminal leader peptide sequence. The translated sequence beginning at the DAF NH2 terminus encodes four contiguous approximately equal to 61-amino acid long repetitive units of internal homology. The repetitive regions contain four conserved cysteines, one proline, one glycine, one glycine/alanine, four leucines/isoleucines/valines, one serine, three tyrosines/phenylalanines, and one tryptophan and show striking homology to similar regions previously identified in factor B, C2, C4 binding protein, factor H, C1r, factor XIII, interleukin 2 receptor, and serum beta 2-glycoprotein I. The consensus repeats are attached to a 70-amino acid long segment rich in serine and threonine (potential O-glycosylation sites), which is in turn followed by a stretch of hydrophobic amino acids. RNA blot analysis of HeLa and HL-60 RNA revealed three DAF mRNA species of 3.1, 2.7, and 2.0 kilobases. The results indicate that portions of the DAF gene may have evolved from a DNA element common to the above proteins, that DAF cDNA predicts a COOH-terminal anchoring polypeptide, and that distinct species of DAF message are elaborated in cells.
Adaptive regulation of intestinal nutrient transporters.
Authors: Diamond J M , Karasov W H
Published: May 2006

Because most eukaryotic somatic cells are bathed in a constant internal milieu, most of their proteins are constitutive, unlike the adaptive enzymes of bacteria. However, intestinal mucosal cells, like bacteria, face a varying milieu. Hence, we tested for adaptive regulation of intestinal nutrient transporters, sought its functional significance, and compared it with regulation of bacterial proteins. All 12 transporters studied proved to be regulated by dietary substrate levels. Regulation in the intestine is slower than in bacteria and shows lower peak-to-basal activity levels. Regulatory patterns vary greatly among transporters: two sugars and two nonessential amino acids monotonically up-regulate their transporters, two vitamins and three minerals monotonically down-regulate their transporters, and two transporters of essential amino acids respond nonmonotonically to levels of their substrates. These varied patterns arise from trade-offs among four factors: transporter costs, calories yielded by metabolizable substrates, fixed daily requirements of essential nutrients, and toxicity of certain nutrients in large amounts. Based on these trade-offs, we predict the form of regulatory pattern for intestinal transporters not yet studied.
Translation of ferritin light and heavy subunit mRNAs is regulated by intracellular chelatable iron levels in rat hepatoma cells.
Authors: Rogers J , Munro H
Published: May 2006

Acute administration of iron to rats has been previously shown to induce liver ferritin synthesis by increasing the translation of inactive cytoplasmic ferritin mRNAs for both heavy (H) and light (L) subunits by mobilizing them onto polyribosomes. In this report rat hepatoma cells in culture are used to explore the relationship of this response to intracellular iron levels. After adding iron as ferric ammonium citrate to the medium, latent ferritin H- and L-mRNAs were extensively transferred to polyribosomes, accompanied by increased uptake of [35S]methionine into ferritin protein. Because total cellular levels of L- and H-mRNA were not significantly changed by exposure to iron, the increased ferritin mRNAs on polyribosomes most probably come from an inactive cytoplasmic pool, consistent with the inability of actinomycin-D and of cordycepin to inhibit iron-induced ferritin synthesis. When deferoxamine mesylate, an intracellular iron chelator, was added after the addition of iron to the medium, ferritin mRNA on the polyribosomes was reduced, while the free messenger pool increased, and ferritin synthesis diminished. In contrast, the extracellular iron chelator diethylenetriaminepentaacetic acid failed to inhibit the induction of ferritin protein synthesis. Addition of iron in the form of hemin also caused translocation of mRNA to polyribosomes, a response that could be similarly quenched by deferoxamine. Because hemin does not release chelatable iron extracellularly, we conclude that the level of chelatable iron within the cell has a regulatory role in ferritin synthesis through redistribution of the messenger RNAs between the free mRNA pool and the polyribosomes.
Isolation of a cDNA clone and localization of human glutathione S-transferase 2 genes to chromosome band 6p12.
Authors: Board P G , Webb G C
Published: May 2006

The glutathione S-transferases (GST) (glutathione transferase; EC 2.5.1.18) are a family of enzymes responsible for the metabolism of a broad range of xenobiotics and carcinogens. A cDNA clone containing the entire amino acid coding sequence of a human GST-2 subunit has been isolated using a lambda gt11 expression library. The complete nucleotide sequence and a partial restriction map are presented. The subunit is composed of 221 amino acids with a molecular weight of 25,425 before posttranslational modification. The deduced amino acid sequence is rich in lysine, which is consistent with the relatively high pI of GST-2. The human sequence shows considerable homology with the rat Ya and Yc GST sequences but little homology with the rat GSTp and Yb subunit sequences. Southern blots of restriction digests of human DNA indicate that there may be multiple GST-2 genes. In situ hybridization of the cloned cDNA to human chromosomes produces intense labeling only over band p12 on the short arm of chromosome 6 near the centromere. This indicates that the GST-2 gene(s) are located only at this site.
Evoked release of acetylcholine from the growing embryonic neuron.
Authors: Sun Y A , Poo M M
Published: May 2006

An excised patch of embryonic muscle membrane was used as a probe for measuring the release of acetylcholine (AcCho) from growing spinal neurons in Xenopus cell culture. The neuron was stimulated extracellularly at the soma, and the evoked AcCho release was monitored at the growth cone, along the neurite, and near the soma. For a majority of the neurons studied, a brief suprathreshold stimulation of the soma triggered a pulse of AcCho release from the growth cone. This release showed many of the characteristics reminiscent of the transmitter release at the nerve terminal of a mature neuromuscular synapse: it occurs within a few ms following the stimulation, depends on extracellular Ca2+ concentration, and exhibits depression and potentiation during and after high-frequency stimulation, respectively. Similar evoked release was also observed only at selected points along the neurite, and prolonged suprathreshold stimulus was required to induce release from the soma. These results indicate that some of the growing spinal neurons have acquired a substantial number of AcCho molecules as well as an efficient mechanism for excitation-secretion coupling at the growth cone, ready for establishing functional contact with the target muscle cell. This notion was further supported by the finding that the evoked AcCho release is capable of inducing suprathreshold excitation of the muscle cell within the first minute following neurite-muscle contact.
Natural UAG suppressor glutamine tRNA is elevated in mouse cells infected with Moloney murine leukemia virus.
Authors: Kuchino Y , Beier H , Akita N , Nishimura S
Published: May 2006

Two species of glutamine tRNA were isolated from mouse liver and their nucleotide sequences were determined. The minor glutamine tRNA(tRNA(UmUGGln)) that possesses UmUG (where Um stands for 2'-O-methyluridine) as the anticodon sequence was found to have suppressor activity for the UAG termination codon of tobacco mosaic virus RNA in a rabbit reticulocyte in vitro translation system. The amount of this suppressor glutamine tRNA in mouse liver was 1-2% of the amount of the major glutamine tRNA(tRNA(CUGGln)) that has the CUG anticodon sequence, but it was markedly increased in NIH 3T3 cells infected with Moloney murine leukemia virus and in Ehrlich ascites cells. These results support the hypothesis that tRNA(UmUGGln) actually functions in vivo as a suppressor tRNA that recognizes the UAG termination codon located at the gag-pol gene junction of Moloney murine leukemia virus and results in the synthesis of the virus-encoded protease.
N-terminal methionine-specific peptidase in Salmonella typhimurium.
Authors: Miller C G , Strauch K L , Kukral A M , Miller J L , Wingfield P T , Mazzei G J , Werlen R C , Graber P , Movva N R
Published: May 2006

Crude extracts of a multiply peptidase-deficient strain of Salmonella typhimurium contain an aminopeptidase that specifically removes N-terminal methionine from peptides. This activity shows pronounced specificity for the peptide's second amino acid. Methionine is removed from peptides with alanine, threonine, or glycine in this position but not when the second amino acid is leucine or methionine. The activity is stimulated by Co2+ and is inhibited by EDTA. Mutations that lead to overproduction (up to 30-fold) of the activity have been obtained by selecting for growth on Met-Gly-Gly as a methionine source. These mutations map at approximately 3 map units, phage P22 cotransducible with leu. The overproducer mutations are dominant to wild type, and duplication of the wild-type allele of the locus leads to a gene dosage effect on peptidase levels. This suggests that the locus of the overproducer mutations may be the structural gene for the peptidase. NaDodSO4/PAGE shows an increased level of a single protein (34 kDa) in the overproducer mutant. This protein is highly enriched in a purified preparation of the peptidase. The specificity of this enzyme suggests that it is involved in the cleavage of methionine from newly synthesized peptide chains. This activity can specifically remove methionine from the N terminus of a completed protein. Treatment of purified, unprocessed (N-terminal methionine) interleukin 1 beta with the purified peptidase results in removal of N-terminal methionine with no additional alterations. N-terminal processing of at least this protein can occur after translation is complete. We propose to call this enzyme peptidase M (methionine-specific aminopeptidase).
Isolation of cDNA clones for the catalytic gamma subunit of mouse muscle phosphorylase kinase: expression of mRNA in normal and mutant Phk mice.
Authors: Chamberlain J S , VanTuinen P , Reeves A A , Philip B A , Caskey C T
Published: May 2006

We have isolated and characterized cDNA clones for the gamma subunit of mouse muscle phosphorylase kinase (gamma-Phk). These clones were isolated from a lambda gt11 mouse muscle cDNA library via screening with a synthetic oligonucleotide probe corresponding to a portion of the rabbit gamma-Phk amino acid sequence. The gamma-Phk cDNA clones code for a 387-amino acid protein that shares 93% amino acid sequence identity with the corresponding rabbit amino acid sequence. RNA gel blot analysis reveals that the muscle gamma-Phk probe hybridizes to two mRNA species (2.4 and 1.6 kilobases) in skeletal muscle, cardiac muscle, and brain, but does not hybridize to liver RNA. Phk-deficient I-strain (Phk) mouse muscle contains reduced levels of gamma-Phk mRNA as compared with control mice. Although the Phk defect is an X-linked recessive trait, hybridization to a human-rodent somatic cell hybrid mapping panel shows that the gamma-Phk gene is not located on the X chromosome. Rather, the gamma-Phk cross-hybridizing human restriction fragments map to human chromosomes 7 (multiple) and 11 (single). Reduced gamma-Phk mRNA in I-strain mice, therefore, appears to be a consequence of the Phk-mutant trait and does not stem from a mutant gamma-subunit gene.
Induction of synthesis of the cytolytic C9 (ninth component of complement)-related protein in human peripheral mononuclear cells by monoclonal antibody OKT3 or interleukin 2: correlation with cytotoxicity and lymphocyte phenotype.
Authors: Martin D E , Zalman L S , Jung G , Müller-Eberhard H J
Published: May 2006

Synthesis of the cytolytic C9-related protein (C9RP) was induced by activation of resting human peripheral T lymphocytes with the anti-CD3 antibody OKT3 or interleukin 2. Comparison of cellular cytotoxicity and C9RP content at various times during activation yielded a coefficient of correlation r = 0.92. During OKT3 stimulation of peripheral mononuclear cells, maximal C9RP content and cytotoxicity were observed by day 2 or 3, with subsequent decline to baseline values by day 5, whereas during interleukin 2 stimulation, both parameters reached the maximal level at days 3-5. After fluorescence-activated cell sorting, C9RP and cytotoxicity were quantitated in CD4+, CD8+, and Leu-19+ subsets. In OKT3-activated CD8+ cells, C9RP increased to approximately 3 X 10(6) molecules per cell, with a corresponding increase in lysis of human melanoma cells mediated by anti-CD3-anti-melanoma monoclonal antibody conjugates. Interleukin 2-stimulated CD8+ cells showed similar increases, but cytotoxicity was conjugate-independent. Activated CD4+ cells showed minimal increase in C9RP content. Leu-19+ cells, which exhibit natural killer cell activity, had a high C9RP content (approximately 2.5 X 10(6) molecules per cell) before stimulation.
Thiol protease-specific inhibitor E-64 arrests human epidermoid carcinoma A431 cells at mitotic metaphase.
Authors: Shoji-Kasai Y , Senshu M , Iwashita S , Imahori K
Published: May 2006

E-64-d (ethyl (2S, 3S)-3-[(S)-3-methyl-1-(3-methylbutylcarbamoyl) butylcarbamoyl]oxirane-2-carboxylate), a membrane-permeant derivative of the thiol protease-specific inhibitor E-64, was found to arrest human epidermoid carcinoma A431 cells at mitotic metaphase. This effect was dose-dependent with a threshold of 20 micrograms/ml in chemically defined culture medium. Cell cycle analysis by flow cytometry showed that the relative proportion of the G2/M population increased 2.5-fold after treatment of the cells with E-64 (100 micrograms/ml) for 5 hr. In addition, time-lapse video analysis showed that E-64-treated cells remained at metaphase for an extended period after rounding-up, whereas untreated cells completed mitosis within 42.0 +/- 5.7 min. Some treated cells were able to complete mitosis, while others did not do so within the limits of our observation. As an approach to the molecular basis of this phenomenon, we have shown that several cellular proteins can be labeled by incubation of cells with radioactive E-64-d.
Analysis by in situ hybridization of cells expressing mRNA for interleukin 4 in the developing thymus and in peripheral lymphocytes from mice.
Authors: Sideras P , Funa K , Zalcberg-Quintana I , Xanthopoulos K G , Kisielow P , Palacios R
Published: May 2006

We have made use of RNA.RNA in situ hybridization to study the presence of cells producing mRNA for interleukin 4 (IL-4) in the developing thymus, spleen, and T-cell line 2.19. Approximately 1 of 300-400 spleen cells expressed detectable IL-4 mRNA 24 hr after their stimulation by the lectin concanavalin A. Spleen cells were also induced to express mRNA for IL-4 by stimulation with alloantigens. Splenocytes producing mRNA for IL-4 were detected 4 hr after stimulation by concanavalin A; the response peaked at approximately equal to 24 hr and was undetectable by 72 hr. Cyclosporin A inhibited the synthesis of IL-4 mRNA in the T-cell line 2.19, which had been induced by concanavalin A. Approximately 1 of 10 fetal thymocytes at day 14 of gestation expressed mRNA for IL-4 after their stimulation by phorbol 12-myristate 13-acetate and ionomycin. Both the frequency of fetal thymocytes expressing IL-4 mRNA and the amount of mRNA for IL-4 synthesized per cell sharply decreased at day 16 of gestation, and less than 1 of 1800 fetal thymocytes at day 18 of gestation expressed detectable IL-4 mRNA. Our results define the relative frequency of cells capable of expressing IL-4 mRNA after stimulation in vitro in the spleen and in the developing thymus. The data strongly argue for an important role of IL-4 in growth and differentiation of lymphoid cells, notably during T-cell development within the thymus.
Cloning and sequencing of cDNAs encoding alpha and beta subunits of human pyruvate dehydrogenase.
Authors: Koike K , Ohta S , Urata Y , Kagawa Y , Koike M
Published: May 2006

The cDNAs encoding fragments of the alpha and beta subunits (PDH alpha and PDH beta) of human pyruvate dehydrogenase (PDH, EC 1.2.4.1) were isolated from a HeLa cell cDNA library in the lambda gt11 expression vector by immunoscreening. Phage cDNA fragments were subsequently used to screen a human foreskin fibroblast cDNA library by colony hybridization. Nucleotide sequence analyses of the positive plasmid clones (pHPDA and pHPDB) revealed an insert of 1.36 kilobases (kb) for PDH alpha and one of 1.69 kb for PDH beta, respectively, allowing us to predict the complete amino acid sequences of the precursor and mature proteins of these two subunits. A putative leader sequence of 29 amino acid residues was identified in pHPDA, resulting in a precursor protein of 392 amino acid residues (Mr 43,414) and a mature protein of 363 residues (Mr 40,334). A similar leader sequence of 30 amino acid residues in pHPDB was also identified, resulting in a precursor protein of 359 amino acid residues (Mr 39,046) and a mature protein of 329 residues (Mr 35,911). The amino acid sequences of NH2-terminal regions of the two subunits of human PDH were highly homologous with those of mature porcine PDH. The amino acid sequences of phosphorylation sites determined in PDH alpha of bovine and porcine enzymes were also conserved in the human PDH alpha. Blot analysis of HeLa cell poly(A)+ RNA showed a single mRNA of 1.8 kb for PDH alpha and 1.7 kb for PDH beta, respectively. The precursor proteins of PDH alpha and PDH beta were detected by immunoprecipitation from an 35S-labeled cell-free translation system.
ATP stimulates the binding of simian virus 40 (SV40) large tumor antigen to the SV40 origin of replication.
Authors: Borowiec J A , Hurwitz J
Published: May 2006

Simian virus 40 (SV40) large tumor antigen (T antigen) binds to two contiguous sites at the SV40 origin of replication. Of these two sites, I and II, only site II is critical for replication. We have studied the interaction between T antigen and these sites by two methods--nitrocellulose filter binding and DNase I protection. We show that T antigen binds with high occupancy to site I at 0 degrees C, 25 degrees C, and 37 degrees C but to site II only at 0 degrees C and 25 degrees C. At 37 degrees C, the temperature essential for the initiation of SV40 DNA replication in vitro, ATP is required for the interaction of T antigen and site II. ATP can be replaced efficiently by adenosine 5'-[beta,gamma-imido]triphosphate and ADP, suggesting that hydrolysis of the nucleotide is not essential for the binding of T antigen to site II. The binding to the region critical for replication can occur in the presence of a variety of nucleoside triphosphates; dATP supports binding at a concentration 1/30th that of ATP, while dGTP and rGTP were inactive at all concentrations tested.
Structural principles of parallel beta-barrels in proteins.
Authors: Lasters I , Wodak S J , Alard P , van Cutsem E
Published: May 2006

Eight-stranded beta-sheets in nine protein structures containing "TIM (triose phosphate isomerase) barrels" are shown to be fitted satisfactorily by hyperboloids, the generating lines of which pass through the beta-strands. Simple parameterizations of the hyperboloid model are then used to determine the constraints that govern key parameters, such as the number of strands in the barrel, and to rationalize the remarkable conservation of strand number, observed to be eight, in nearly all the known examples of parallel beta-barrels. It is shown that the requirement to exclude solvent from the barrel interior, while at the same time keeping an upper limit on strand twist and interstrand distance so as to foster extensive hydrogen bonding interactions within the sheet, imposes strong constraints on barrel geometry. A formal description of the relationships between beta-sheet twist, strand number, and barrel dimensions is given here. It could have important implications for studies of protein folding and design.
Cloning and characterization of a potentially protective antigen in lymphatic filariasis.
Authors: Nilsen T W , Maroney P A , Goodwin R G , Perrine K G , Denker J A , Nanduri J , Kazura J W
Published: May 2006

To facilitate biochemical studies of protective filarial antigens, a lambda gt11 cDNA library was constructed from Brugia malayi adult mRNA and screened with rabbit sera that recognizes a limited set of filarial antigens of approximately 25, 42, 60, and 112 kDa. Antigens of approximately equal to 25 and approximately equal to 60 kDa have been shown previously to induce enhanced clearance of microfilaremia in mice. A 154-base pair clone detected by immunological reactivity was used to isolate by hybridization a nearly full-length cDNA clone of 1.8 kilobases. Nucleotide-sequence analysis indicated that this clone was derived from a mRNA encoding a 63-kDa antigen. A fusion polypeptide containing 37 kDa of the Escherichia coli TrpE protein (anthranilate synthase) and 55 kDa of the cloned protein was recognized in immunoblot experiments with antisera raised against a partially purified preparation of the approximately equal to 60-kDa protective filarial antigen. These data relate the cloned antigen to a potentially protective antigen in lymphatic filariasis.
Neuroanatomical localization and quantification of amyloid precursor protein mRNA by in situ hybridization in the brains of normal, aneuploid, and lesioned mice.
Authors: Bendotti C , Forloni G L , Morgan R A , O'Hara B F , Oster-Granite M L , Reeves R H , Gearhart J D , Coyle J T
Published: May 2006

Amyloid precursor protein mRNA was localized in frozen sections from normal and experimentally lesioned adult mouse brain and from normal and aneuploid fetal mouse brain by in situ hybridization with a 35S-labeled mouse cDNA probe. The highest levels of hybridization in adult brain were associated with neurons, primarily in telencephalic structures. The dense labeling associated with hippocampal pyramidal cells was reduced significantly when the cells were eliminated by injection of the neurotoxin ibotenic acid but was not affected when electrolytic lesions were placed in the medial septum. Since the gene encoding amyloid precursor protein has been localized to mouse chromosome 16, we also examined the expression of this gene in the brains of mouse embryos with trisomy 16 and trisomy 19 at 15 days of gestation. RNA gel blot analysis and in situ hybridization showed a marked increase in amyloid precursor protein mRNA in the trisomy 16 mouse head and brain when compared with euploid littermates or with trisomy 19 mice.
Guanine nucleotide-binding protein Go-induced coupling of neuropeptide Y receptors to Ca2+ channels in sensory neurons.
Authors: Ewald D A , Sternweis P C , Miller R J
Published: May 2006

Neuropeptide Y (NPY) inhibited the Ca2+ current (ICa) in rat dorsal root ganglion neurons in vitro. NPY inhibited the sustained ICa evoked by steps to 0 mV from a holding potential of -40 mV and the inactivating ICa, which was additionally evoked from a more negative holding potential of -80 mV. The effects of NPY on both phases of the ICa were abolished if cells were first treated with pertussis toxin (PTX). When a combination of GTP and the purified alpha-subunit of the guanine nucleotide-binding protein Go was perfused into PTX-treated cells, the inhibitory effects of NPY on the ICa reappeared in a time-dependent fashion. GTP or alpha-subunit perfused separately was relatively ineffective. The effects of NPY reappeared more rapidly at higher concentrations of alpha o. Chronic treatment of these cells with phorbol ester "down-regulates" protein kinase C (PKC) and reduces inhibition of the sustained current by NPY. In PTX-treated cells in which PKC had been removed by down-regulation, inhibition of ICa was also reconstituted following the perfusion of GTP/alpha o. Under these circumstances, NPY inhibited the transient phase of the ICa more than the sustained phase. These results indicate that Go, the major PTX substrate in the central nervous system, may normally mediate the inhibitory effects of NPY receptors on dorsal root ganglion Ca2+ channels.
Estimating a treatment effect under biased sampling.
Authors: Robbins H , Zhang C H
Published: May 2006

Methods are presented for the estimation of a treatment effect based on before- and after-treatment values, where for ethical reasons all and only those patients are treated whose before-treatment values exceed a given constant.
Activation of ras oncogene in aflatoxin-induced rat liver carcinogenesis.
Authors: Sinha S , Webber C , Marshall C J , Knowles M A , Proctor A , Barrass N C , Neal G E
Published: May 2006

The presence of activated transforming genes was investigated in four primary aflatoxin-induced rat liver tumors in male Fischer rats, in two cell lines generated from such tumors, in an epithelial liver-derived nontransformed cell line, and in the latter cell line after transformation by aflatoxin B1 in vitro. When DNA extracted from these sources was transfected into NIH 3T3 cells, negative results were obtained from focus assays. Cotransfection of these DNA samples with a gene for resistance to G418, followed by selection for resistance to that antibiotic, and tumorigenicity testing in nude mice demonstrated DNA-mediated transfer of the neoplastic phenotype in all cases except for DNA from the nontransformed cell line. DNA extracted from these primary nude mouse tumors used in a secondary round of transfection with NIH 3T3 cells gave positive results in focus assays, which were conserved through succeeding rounds of transfection. By use of appropriate radiolabeled probes, activated ras oncogenes were detected in all samples. N-ras activation was detected in three of the primary rat liver tumors and both hepatoma cell lines. Ki-ras activation was detected in one primary rat liver tumor, and Ha-ras activation was detected in the cell line transformed in vitro with activated aflatoxin B1. The activated Ki-ras oncogene was further characterized by use of synthetic oligonucleotide probes and was shown to contain a G----A transition at the second nucleotide in codon 12.
A receptor model for tumor promoters: rational superposition of teleocidins and phorbol esters.
Authors: Itai A , Kato Y , Tomioka N , Iitaka Y , Endo Y , Hasegawa M , Shudo K , Fujiki H , Sakai S
Published: May 2006

Four 12-O-tetradecanoyl-13-O-acetylphorbol-type tumor promoters--teleocidin, phorbol ester, aplysiatoxin, and ingenol ester--are superposed in an attempt to understand their common biological activity on the assumption that they may bind to the same receptor site. A method using three-dimensional computer graphics was applied for superposing molecules and receptor mapping. The main feature of the method is that molecules are superposed in terms of spatial arrangement of physical and chemical properties but not in terms of the atomic positions as in conventional methods. This led to successful extraction of common structural features required for potent tumor-promoting activity: two hydrogen donors, a hydrogen acceptor, and a large lipophilic group. Their mutual spatial arrangements are most important for biological activity.
Genetic characterization of a brain-specific form of the type I regulatory subunit of cAMP-dependent protein kinase.
Authors: Clegg C H , Cadd G G , McKnight G S
Published: May 2006

An isoform (RI beta) of the regulatory type I subunit gene of cAMP-dependent protein kinase (EC 2.7.1.37) has been characterized in mouse. The open reading frame of the RI beta cDNA is 72% identical in nucleotide sequence with the previously cloned RI gene, now referred to as RI alpha. Both genes code for a protein of 380 amino acids and their proteins are 82% identical in amino acid sequence. Sequence similarity is highest in the regions that form the pseudosubstrate-binding site of the catalytic subunit and the two cAMP binding domains. The amino-terminal portion shows the greatest dissimilarity, suggesting that the isoforms may differ in their dimerization properties or interaction with other proteins. In contrast to RI alpha, which is constitutively expressed in all tissues, RI beta is expressed in a highly tissue-specific manner. Brain and spinal cord contained significant levels of RI beta mRNA, testis RNA gave a detectable signal, and all other tissues tested were negative. Expression of a RI beta cDNA in NIH 3T3 cells resulted in the appearance of a RI subunit protein that migrated more slowly than RI alpha after NaDodSO4/PAGE. The native form of RI beta in brain could also be distinguished from RI alpha by its abnormal migration on NaDodSO4/PAGE. RI beta protein produced in 3T3 cells was shown to be functional by its ability to form a cAMP-dependent holoenzyme with the catalytic subunit.
Electron microscopic study of crystals of the Xenopus laevis transcription factor IIIA-5S ribosomal RNA complex.
Authors: Brown R S , Ferguson C , Kingswell A , Winkler F K , Leonard K R
Published: May 2006

A novel method has been developed to grow crystals of the Xenopus laevis transcription factor IIIA-5S RNA complex directly on grids for examination by electron microscopy. Microcrystals were examined in negative stain and in thin sections to reveal a hexagonal lattice with unit-cell dimensions a = b = 87.1 +/- 4.4 A and c = 143.8 +/- 12.7 A. Optical diffraction patterns from micrographs were obtained about the major crystal axes extending to about 40-A resolution. A packing scheme is proposed for which there are three or six transcription factor IIIA-5S RNA complexes in the unit cell related by 3(1) symmetry along the long cell axis. This would require that the 5S RNA molecules are arranged end-to-end, with the terminal loops of adjacent molecules overlapping.
Molecular cloning and nucleotide sequence of cDNA for human glucose-6-phosphate dehydrogenase variant A(-).
Authors: Hirono A , Beutler E
Published: May 2006

Glucose-6-phosphate dehydrogenase (G6PD; D-glucose-6-phosphate:NADP+ oxidoreductase, EC 1.1.1.49) A(-) is a common variant in Blacks that causes sensitivity to drug-and infection-induced hemolytic anemia. A cDNA library was constructed from Epstein-Barr virus-transformed lymphoblastoid cells from a male who was G6PD A(-). One of four cDNA clones isolated contained a sequence not found in the other clones nor in the published cDNA sequence. Consisting of 138 bases and coding 46 amino acids, this segment of cDNA apparently is derived from the alternative splicing involving the 3' end of intron 7. Comparison of the remaining sequences of these clones with the published sequence revealed three nucleotide substitutions: C33----G, G202----A, and A376----G. Each change produces a new restriction site. Genomic DNA from five G6PD A(-) individuals was amplified by the polymerase chain reaction. The base substitution at position 376, identical to the substitution that has been reported in G6PD A(+), was present in all G6PD A(-) samples and none of the control G6PD B(+) samples examined. The substitution at position 202 was found in four of the five G6PD A(-) samples and no normal control sample. At position 33 guanine was found in all G6PD A(-) samples and seven G6PD B(+) control samples and is, presumably, the usual nucleotide found at this position. The finding of the same mutation in G6PD A(-) as is found in G6PD A(+) strongly suggests that the G6PD A(-) mutation arose in an individual with G6PD A(+), adding another mutation that causes the in vivo instability of this enzyme protein.
Inhibition of methyltransferase reduces the turnover of acetylcholine receptors.
Authors: Kuncl R W , Drachman D B , Adams R
Published: May 2006

Because of the putative rule of phospholipid methyltransferase reactions in many important membrane and receptor translocation processes, we studied the effect of methyltransferase inhibitors on acetylcholine receptor (AcChoR) turnover in cultured rat skeletal muscle. Inhibition of methyltransferase significantly reduced the normal rate of degradation of AcChoRs, a process that involves endocytosis. Further, under conditions that greatly accelerate the rate of degradation of AcChoRs--i.e., by addition of anti-AcChoR antibody--methyltransferase inhibitors again significantly reduced receptor turnover. AcChoR synthesis was unaffected. Thus, the net effect of this treatment was slowing of the antibody-induced loss of surface AcChoRs. That this drug effect was mediated specifically by inhibition of methylation reactions was suggested by certain additional pharmacologic features: partial reversibility of the effect by methionine, enhancement by homocysteine, and correspondence with marked inhibition of phospholipid methylation. The substrate specificity of the methyltransferase inhibitors capable of reducing AcChoR degradation suggests that phospholipid methylation reactions may be most relevant. Methyltransferase inhibitor drugs may provide a therapeutic strategy in receptor disorders such as myasthenia gravis, in which accelerated receptor endocytosis plays a major role.
Oncogene v-src transforms and establishes embryonic rodent fibroblasts but not diploid human fibroblasts.
Authors: Hjelle B , Liu E , Bishop J M
Published: May 2006

The conversion of cells from a normal phenotype to full malignancy apparently requires multiple genetic events. Efforts to reconstruct multistep tumorigenesis in cell culture have shown that two types of oncogenes (typified by HRAS and MYC) can cooperate to elicit complete transformation. Transformation of embryonic rodent cells by single oncogenes is reputed either not to occur or to require specialized circumstances. It has not been known how the large group of oncogenes that encode protein-tyrosine kinases might fit into this scheme. We now report that v-src, a prototype for the kinase oncogenes, can convert rat embryo fibroblasts to a fully transformed and tumorigenic phenotype when the gene is expressed vigorously. By contrast, v-src had no demonstrable effect on diploid human fibroblasts. Our results sustain the view that it is possible for at least some oncogenes to achieve a potency sufficient for unilateral tumorigenesis.
Analysis in serum-free culture of the targets of recombinant human hemopoietic growth factors: interleukin 3 and granulocyte/macrophage-colony-stimulating factor are specific for early developmental stages.
Authors: Sonoda Y , Yang Y C , Wong G G , Clark S C , Ogawa M
Published: May 2006

We have used a serum-free culture system for enriched human hemopoietic progenitors to analyze the developmental stages and lineage specificities of the human hemopoietic colony-stimulating factors. None of the individual factors alone efficiently supported hemopoietic colony formation. Neither interleukin 3 nor granulocyte/macrophage-colony-stimulating factor alone or in combination effectively supported proliferation of progenitor cells. However, when combined with granulocyte-colony-stimulating factor or erythropoietin, these factors yielded neutrophil colonies or erythroid bursts, respectively. Serial observations of interleukin 3-supported cultures revealed sequential emergence and subsequent degeneration of clusters of cells. These observations suggest that the primary targets of interleukin 3 and granulocyte/macrophage-colony-stimulating factor are multipotent progenitors at the early stages of development rather than cells in the terminal process of maturation.