bluuebunny/crossref_metadata_2025 huggingface dataset:
A third human retinoic acid receptor, hRAR-gamma.
Authors: Krust A , Kastner P , Petkovich M , Zelent A , Chambon P
Published: May 2006

Retinoic acid receptors (RARs) are retinoic acid (RA)-inducible enhancer factors belonging to the superfamily of steroid/thyroid nuclear receptors. We have previously characterized two human RAR (hRAR-alpha and hRAR-beta) cDNAs and have recently cloned their murine cognates (mRAR-alpha and mRAR-beta) together with a third RAR (mRAR-gamma) whose RNA was detected predominantly in skin, a well-known target for RA. mRAR-gamma cDNA was used here to clone its human counterpart (hRAR-gamma) from a T47D breast cancer cell cDNA library. Using a transient transfection assay in HeLa cells and a reporter gene harboring a synthetic RA responsive element, we demonstrate that hRAR-gamma cDNA indeed encodes a RA-inducible transcriptional trans-activator. Interestingly, comparisons of the amino acid sequences of all six human and mouse RARs indicate that the interspecies conservation of a given member of the RAR subfamily (either alpha, beta, or gamma) is much higher than the conservation of all three receptors within a given species. These observations indicate that RAR-alpha, -beta, and -gamma may perform specific functions. We show also that hRAR-gamma RNA is the predominant RAR RNA species in human skin, which suggests that hRAR-gamma mediates some of the retinoid effects in this tissue.
Genomic footprinting in mammalian cells with ultraviolet light.
Authors: Becker M M , Wang Z , Grossmann G , Becherer K A
Published: May 2006

A simple and accurate genomic primer extension method has been developed to detect ultraviolet footprinting patterns of regulatory protein-DNA interactions in mammalian genomic DNA. The technique can also detect footprinting or sequencing patterns introduced into genomic DNA by other methods. Purified genomic DNA, containing either damaged bases or strand breaks introduced by footprinting or sequencing reactions, is first cut with a convenient restriction enzyme to reduce its molecular weight. A highly radioactive single-stranded DNA primer that is complementary to a region of genomic DNA whose sequence or footprint one wishes to examine is then mixed with 50 micrograms of restriction enzyme-cut genomic DNA. The primer is approximately 100 bases long and contains 85 radioactive phosphates, each of specific activity 3000 Ci/mmol (1 Ci = 37 GBq). A simple and fast method for preparing such primers is described. Following brief heat denaturation at 100 degrees C, the solution of genomic DNA and primer is cooled to 74 degrees C and a second solution containing Taq polymerase (Thermus aquaticus DNA polymerase) and the four deoxynucleotide triphosphates is added to initiate primer extension of genomic DNA. Taq polymerase extends genomic hybridized primer until its polymerization reaction is terminated either by a damaged base or strand break in genomic DNA or by the addition of dideoxynucleotide triphosphates in the polymerization reaction. The concurrent primer hybridization-extension reaction is terminated after 5 hr and unhybridized primer is digested away by mung bean nuclease. Primer-extended genomic DNA is then denatured and electrophoresed on a polyacrylamide sequencing gel, and radioactive primer extension products are revealed by autoradiography. By using this method we demonstrate that it is possible to footprint with ultraviolet light, in intact monkey cells, regulatory protein--DNA interactions along a single copy of a simian virus 40 viral genome integrated into the monkey genome.
Telomeric function of the tRNA-like structure of brome mosaic virus RNA.
Authors: Rao A L , Dreher T W , Marsh L E , Hall T C
Published: May 2006

Four mutant brome mosaic virus (BMV) RNA3 transcripts, bearing single or double base changes in the 3'-CCAOH terminus of the tRNA-like structure, previously characterized as being deficient in vitro with respect to aminoacylation and replication activities, have now been assayed in vivo for their ability to replicate (in the presence of transcripts of wild-type RNA1 and -2) in barley protoplasts and plants. In tests conducted with protoplasts, irrespective of the time post-infection, all four mutants were fully viable, and the relative levels of both plus and minus strand replication for each mutant were similar to that of the wild type. Inoculation of barley plants with these mutants resulted in phenotypic symptoms and viral yields that were similar to those from wild-type infections. Analysis of each mutant progeny RNA3 indicated that the altered sequence at the 3' terminus was restored to that of wild type. These observations indicate that there is a rapid turnover and correction of the 3' termini of BMV RNAs in vivo. Such correction is commensurate with the action of tRNA nucleotidyltransferase, but it differs from recombination processes that appear to be relatively infrequent for BMV RNA3. These results support the conclusion that the 3'-CCAOH termini of viral tRNA-like structures function analogously to telomeres of chromosomal DNA.
Mechanism of spontaneous vesiculation.
Authors: Hauser H
Published: May 2006

Both naturally occurring and synthetic phosphatidic acid (PtdOH) molecules show the phenomenon of spontaneous vesiculation on jump in pH value. This method involves a transient increase in pH of smectic PtdOH dispersions to values between 10 and 12. Such a pH increase induces spontaneous vesiculation with the formation of small unilamellar vesicles of diameter less than 50 nm as shown by 31P NMR. Both high-resolution and broad-line 31P NMR were used to study the mechanism of this process. When the pH of unsonicated PtdOH dispersions is raised to pH 10-12, lipid molecules on the outer monolayer of the bilayer become fully ionized. The second pK value of PtdOH in bilayers is 8.6 +/- 0.3, determined by 31P NMR. PtdOH molecules on the inner monolayer remain partially protonated. 31P NMR provides unambiguous evidence that the "pH-jump" treatment produces a pH gradient across the PtdOH bilayer. The orientation of the pH gradient is such that the pH in the external medium is 3-5 pH units higher than the internal pH. Associated with the pH gradient is a transverse packing asymmetry: partially protonated PtdOH molecules in the inner layer of the bilayer are more tightly packed than fully ionized molecules present in the outer layer. The pH gradient generated by the pH jump is proposed as the energy source that drives the spontaneous formation of highly curved vesicles.
Formation of hybrid cell-cell channels.
Authors: Werner R , Levine E , Rabadan-Diehl C , Dahl G
Published: May 2006

The oocyte cell-cell channel assay was used to demonstrate that connexin-43 is a cell-cell channel-forming protein as previously shown for connexin-32. Expression of connexin-32 in one and connexin-43 in the other oocyte of a pair results in the formation of junctional conductances at rates similar to those observed when only one or the other connexin is expressed in both oocytes of a pair. This suggests that hybrid cell-cell channels form in the oocyte system. Hybrid channels also form when a connexin-43 mRNA-injected oocyte is paired with a noninjected oocyte expressing endogenous connexin. The latter hybrids have properties apparently contributed by both types of hemichannels. Pure connexin-43 channels are not voltage gated, whereas pure oocyte channels are voltage dependent; hybrids of these channels rectify.
Molecular analysis of the human beta-globin locus activation region.
Authors: Forrester W C , Novak U , Gelinas R , Groudine M
Published: May 2006

Recently, DNA sequences containing four erythroid-specific DNase I hypersensitive sites within 20 kilobases 5' of the human epsilon-globin gene have been identified as an important cis-acting regulatory element, the locus activation region (LAR). Subfragments of the LAR, containing either all or only the two 5' or two 3' hypersensitive sites were linked to the human beta-globin gene and analyzed for their effect on globin gene expression in stably transformed mouse erythroleukemia (MEL) cells. Constructs containing all four of the hypersensitive sites increase beta-globin mRNA levels 8- to 13-fold, while constructs with only the 5' or 3' sites increase globin expression to a lesser extent. No effect was seen when the constructs were assayed in 3T3 fibroblasts. All of the LAR derivatives form hypersensitive sites at the corresponding sequence position in MEL cells prior to and after induction of MEL cell differentiation. However, in 3T3 fibroblasts only the hypersensitive site corresponding to the previously described erythroid-specific -10.9 site was formed.
Abnormal development and dye coupling produced by antisense RNA to gap junction protein in mouse preimplantation embryos.
Authors: Bevilacqua A , Loch-Caruso R , Erickson R P
Published: May 2006

Antisense RNA to the 27/32-kDa rat liver gap junction (GJ) protein was used to explore the role of GJs in preimplantation embryos. When all blastomeres of two- and four-cell embryos were injected with GJ antisense RNA, the percentage of embryos compacted at 60 hr of development was reduced to less than 20%, while 90% of uninjected embryos and 75% of embryos injected with an unrelated RNA were compacted. When most cells of compacted eight-cell embryos were injected with the GJ antisense RNA, 20% of the embryos were decompacted and only 5% had developed to the blastocyst stage at 90 hr, when blastulation had occurred in 90% of the control embryos. When antisense RNA was injected in one blastomere of four-cell embryos, 40% of the embryos presented a large cell that was not included in the compacted embryo at the time of compaction, and an additional 30% of the embryos had two smaller, excluded blastomeres. These excluded cells were identified as the injected cell with a rhodamine-conjugated dextran marker. To assess effects on junctional communication, one blastomere of some embryos was injected with Lucifer yellow, a GJ-penetrating dye, at various times after a blastomere was injected with antisense RNA. The dye was visible in the whole cell mass of control embryos, but it was excluded from a portion of experimental embryos when the delay between the RNA and the Lucifer yellow injections was 1 hr or longer.
Activation of the Mlvi-1/mis1/pvt-1 locus in Moloney murine leukemia virus-induced T-cell lymphomas.
Authors: Tsichlis P N , Shepherd B M , Bear S E
Published: May 2006

The Mlvi-1/mis-1/pvt-1 locus, located approximately 270 kilobase pairs 3' of the c-myc protooncogene, was originally discovered as a common region of provirus integration in Moloney murine leukemia virus-induced rat T-cell lymphomas. The same locus was shown subsequently to be coamplified with c-myc and to be involved in chromosomal translocations in a variety of human and animal neoplasms. Provirus integration in Mlvi-1 in Moloney murine leukemia virus-induced rat T-cell lymphomas activates the c-myc protooncogene. The studies reported here were aimed to determine whether, in addition to the activation of c-myc, provirus integration affected the expression of other neighboring genes. Provirus integration was shown to occur in three clusters separated by regions of uninterrupted DNA. The proviruses in all three clusters had integrated in a single-transcriptional orientation, and they appeared intact. Systematic hybridization of Mlvi-1 clones to rat, mouse, and human genomic DNA revealed three patches of evolutionarily conserved sequences. Two of them were mapped in regions targeted by the provirus, and the third was mapped immediately 5' to the provirus clusters. A probe derived from the conserved sequences 5' of the integrated proviruses detected a tumor-specific RNA transcript in tumors carrying a provirus in Mlvi-1 or in the neighboring Mlvi-4 and c-myc loci. The highest level of RNA transcript expression, however, was seen in a CD4+ CD8+ tumor cell line that was not carrying a provirus in this region. We conclude that provirus insertion in this region activates both c-myc and another gene that is located in the immediate vicinity of the integrated Mlvi-1 proviruses and may be developmentally regulated in T cells.
Monoclonal antibody against interferon gamma can prevent experimental cerebral malaria and its associated overproduction of tumor necrosis factor.
Authors: Grau G E , Heremans H , Piguet P F , Pointaire P , Lambert P H , Billiau A , Vassalli P
Published: May 2006

Experimental cerebral malaria (ECM), a lethal hyperacute neurological syndrome associated with high blood levels of tumor necrosis factor, develops in genetically susceptible (CBA/Ca) mice 7 days after infection with Plasmodium berghei ANKA strain. Injections of neutralizing monoclonal antibody against recombinant murine interferon gamma, not later than 4 days after infection, markedly reduced the incidence of ECM and the elevation in serum levels of tumor necrosis factor. This treatment prevented the cerebral lesions (plugging of brain vessels by monocytes, lymphocytes, and parasitized erythrocytes). In contrast, the extent of macrophage infiltration in lymphoid organs (which is a characteristic feature of mice developing ECM), as well as the course of infection, remained unaffected by the antibody treatment. Protected mice died at a later time of severe anemia and overwhelming parasitemia, the usual outcome of P. berghei infection in mice that are not susceptible to ECM. The present data indicate that interferon gamma constitutes an important link in the cytokine network that leads to brain vessel inflammation in experimental malaria. It is proposed that interferon gamma released by activated CD4+ T cells acts by augmenting both production and action of tumor necrosis factor.
Antibiotic proteins of human polymorphonuclear leukocytes.
Authors: Gabay J E , Scott R W , Campanelli D , Griffith J , Wilde C , Marra M N , Seeger M , Nathan C F
Published: May 2006

Nine polypeptide peaks with antibiotic activity were resolved from human polymorphonuclear leukocyte azurophil granule membranes. All but 1 of the 12 constituent polypeptides were identified by N-terminal sequence analysis. Near quantitative recovery of protein and activity permitted an assessment of the contribution of each species to the overall respiratory-burst-independent antimicrobial capacity of the cell. Three uncharacterized polypeptides were discovered, including two broad-spectrum antibiotics. One of these, a defensin that we have designated human neutrophil antimicrobial peptide 4, was more potent than previously described defensins but represented less than 1% of the total protein. The other, named azurocidin, was abundant and comparable to bactericidal permeability-increasing factor in its contribution to the killing of Escherichia coli.
One-sided polymerase chain reaction: the amplification of cDNA.
Authors: Ohara O , Dorit R L , Gilbert W
Published: May 2006

We report a rapid technique, based on the polymerase chain reaction (PCR), for the direct targeting, enhancement, and sequencing of previously uncharacterized cDNAs. This method is not limited to previously sequenced transcripts, since it requires only two adjacent or partially overlapping specific primers from only one side of the region to be amplified. These primers can be located anywhere within the message. The specific primers are used in conjunction with nonspecific primers targeted either to the poly(A)+ region of the message or to an enzymatically synthesized d(A) tail. Pairwise combinations of specific and general primers allow for the amplification of regions both 3' and 5' to the point of entry into the message. The amplified PCR products can be cloned, sequenced directly by genomic sequencing, or labeled for sequencing by amplifying with a radioactive primer. We illustrate the power of this approach by deriving the cDNA sequences for the skeletal muscle alpha-tropomyosins of European common frog (Rana temporaria) and zebrafish (Brachydanio rerio) using only 300 ng of a total poly(A)+ preparation. In these examples, we gained initial entry into the tropomyosin messages by using heterologous primers (to conserved regions) derived from the rat skeletal muscle alpha-tropomyosin sequence. The frog and zebrafish sequences are used in an analysis of tropomyosin evolution across the vertebrate phylogenetic spectrum. The results underscore the conservative nature of the tropomyosin molecule and support the notion of a constrained heptapeptide unit as the fundamental structural motif of tropomyosin.
Homology of the human intestinal Na+/glucose and Escherichia coli Na+/proline cotransporters.
Authors: Hediger M A , Turk E , Wright E M
Published: May 2006

Cotransport proteins are responsible for the active accumulation of organic substrates in cells. Na+ gradients provide the driving force for uptake of most substrates into eukaryotes and for a few substrates in some prokaryotes. We report here the cloning and sequencing of the human intestinal Na+/glucose cotransporter (SGLT1) and compare its structure with other cloned transporters. At the DNA level and the predicted amino acid and secondary structure levels, close homology is evident between the human and rabbit intestinal Na+/glucose cotransporters, and a significant homology is found between these and the Escherichia coli Na+/proline cotransporter (putP). No homology is detectible with other known proteins. We infer from these results that the mammalian Na+/glucose and prokaryote Na+/proline cotransporters share a common ancestral gene.
Autoregulatory control of beta-tubulin mRNA stability is linked to translation elongation.
Authors: Gay D A , Sisodia S S , Cleveland D W
Published: May 2006

Tubulin synthesis in animal cells is controlled in part by an autoregulatory mechanism that modulates the stability of ribosome-bound tubulin mRNAs. For beta tubulin, the initial recognition event for this selective RNA instability has previously been shown to be a cotranslational binding (presumably by tubulin itself) to the nascent amino-terminal beta-tubulin tetrapeptide just after it emerges from the ribosome. Although this "autoregulation" of tubulin expression is thus obligatorily linked to the translation process, the mechanism of how a cotranslational protein-protein binding event ultimately triggers RNA degradation is unknown. Using protein synthesis inhibitors to slow and ultimately to block translation elongation, we now show that the mRNA destabilization pathway requires ongoing ribosome translocation.
Phorbol 12-myristate 13-acetate inhibits binding of leukotriene B4 and platelet-activating factor and the responses they induce in neutrophils: site of action.
Authors: Yamazaki M , Gomez-Cambronero J , Durstin M , Molski T F , Becker E L , Sha'afi R I
Published: May 2006

The addition of the platelet-activating factor (PAF) to neutrophils causes an increase in cytoskeletal actin, a rise in the intracellular concentration of free calcium, release of arachidonic acid, and the synthesis of PAF. The PAF synthesis in human neutrophils stimulated by PAF is greatly potentiated by the human granulocyte-macrophage colony-stimulating factor. Incubation of human neutrophils with the tumor copromoter phorbol 12-myristate 13-acetate (PMA) for 3 min prior to the addition of the stimulus inhibits all these responses produced by PAF. The inhibition is prevented when the cells are incubated with protein kinase C inhibitors such as 1-(5-isoquinolinesulfonyl)-2-methylpiperazine for 5 min prior to the addition of PMA. The rise in the intracellular concentration of free calcium in human neutrophils stimulated with leukotriene B4 is also inhibited by PMA, and this inhibition is prevented by protein kinase C inhibitors such as staurosporine. Unlike PMA, the inactive ester 4 alpha-phorbol 12,13-didecanoate has no inhibitory effect on the stimulated rise in the intracellular concentration of free calcium. The binding of either PAF or leukotriene B4 to intact cells is inhibited by PMA. The most important finding of the present studies is that PMA interferes with the binding of PAF and leukotriene B4 to their respective receptors. Whether PMA inhibits the binding of these lipid mediators by activating protein kinase C or by perturbing the membrane directly remains to be elucidated.
Recognition of a self major histocompatibility complex TL region product by gamma delta T-cell receptors.
Authors: Bonneville M , Ito K , Krecko E G , Itohara S , Kappes D , Ishida I , Kanagawa O , Janeway C A , Murphy D B , Tonegawa S
Published: May 2006

Ligand specificity of a murine gammadelta T-cell receptor-expressing hybridoma (KN6) derived from adult thymocytes has been analyzed in detail. The molecule recognized by the KN6 gammadelta T-cell receptor is expressed on syngeneic cells of various sources (peritoneal macrophages, thymocytes, spleen cells, and Abelson murine leukemia virus-transformed cell lines) and on transformed cells arrested at an early stage of development (e.g., PCC3 embryonal carcinoma cells). Linkage of the gene coding for the KN6 ligand to the major histocompatibility complex genes could be demonstrated by testing KN6 hybridoma reactivity to cells from congenic strains that differ only at H-2. In addition, analysis of recombinant strains indicates that the gene controlling the KN6 ligand is located in or distal to the TL region. Involvement of the KN6 gammadelta T-cell receptor in this recognition process could be directly demonstrated by transferring the KN6 TL specificity after introduction of the productively rearranged KN6 gamma and delta genes into an alphabeta T-cell clone or into the germ line in transgenic mice. These observations raise the possibility that at least some gammadelta cells regulate hemopoietic cell maturation and activation.
Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex.
Authors: Padlan E A , Silverton E W , Sheriff S , Cohen G H , Smith-Gill S J , Davies D R
Published: May 2006

The crystal structure of the complex of the anti-lysozyme HyHEL-10 Fab and hen egg white lysozyme has been determined to a nominal resolution of 3.0 A. The antigenic determinant (epitope) on the lysozyme is discontinuous, consisting of residues from four different regions of the linear sequence. It consists of the exposed residues of an alpha-helix together with surrounding amino acids. The epitope crosses the active-site cleft and includes a tryptophan located within this cleft. The combining site of the antibody is mostly flat with a protuberance made up of two tyrosines that penetrate the cleft. All six complementarity-determining regions of the Fab contribute at least one residue to the binding; one residue from the framework is also in contact with the lysozyme. The contacting residues on the antibody contain a disproportionate number of aromatic side chains. The antibody-antigen contact mainly involves hydrogen bonds and van der Waals interactions; there is one ion-pair interaction but it is weak.
Critical role of the D21S55 region on chromosome 21 in the pathogenesis of Down syndrome.
Authors: Rahmani Z , Blouin J L , Creau-Goldberg N , Watkins P C , Mattei J F , Poissonnier M , Prieur M , Chettouh Z , Nicole A , Aurias A
Published: May 2006

The duplication of a specific region of chromosome 21 could be responsible for the main features of Down syndrome. To define and localize this region, we analyzed at the molecular level the DNA of two patients with partial duplication of chromosome 21. These patients belong to two groups of Down syndrome patients characterized by different partial trisomies 21: (i) duplication of the long arm, proximal to 21q22.2, and (ii) duplication of the end of the chromosome, distal to 21q22.2 We assessed the copy number of five chromosome 21 sequences (SOD1, D21S17, D21S55, ETS2, and D21S15) and found that D21S55 was duplicated in both cases. By means of pulsed-field gel analysis and with the knowledge of regional mapping of the probes D21S17, D21S55 and ETS2, we estimated the size of the common duplicated region to be between 400 and 3000 kilobases. This region, localized on the proximal part of 21q22.3, is suspected to contain genes the overexpression of which is crucial in the pathogenesis of Down syndrome.
Studies of the mechanisms of action of the antiretroviral agents hypericin and pseudohypericin.
Authors: Lavie G , Valentine F , Levin B , Mazur Y , Gallo G , Lavie D , Weiner D , Meruelo D
Published: May 2006

Administration of the aromatic polycyclic dione compounds hypericin or pseudohypericin to experimental animals provides protection from disease induced by retroviruses that give rise to acute, as well as slowly progressive, diseases. For example, survival from Friend virus-induced leukemia is significantly prolonged by both compounds, with hypericin showing the greater potency. Viremia induced by LP-BM5 murine immunodeficiency virus is markedly suppressed after infrequent dosage of either substance. These compounds affect the retroviral infection and replication cycle at least at two different points: (i) Assembly or processing of intact virions from infected cells was shown to be affected by hypericin. Electron microscopy of hypericin-treated, virus-producing cells revealed the production of particles containing immature or abnormally assembled cores, suggesting the compounds may interfere with processing of gag-encoded precursor polyproteins. The released virions contain no detectable activity of reverse transcriptase. (ii) Hypericin and pseudohypericin also directly inactivate mature and properly assembled retroviruses as determined by assays for reverse transcriptase and infectivity. Accumulating data from our laboratories suggest that these compounds inhibit retroviruses by unconventional mechanisms and that the potential therapeutic value of hypericin and pseudohypericin should be explored in diseases such as AIDS.
Characterization of a RNA virus from the parasite Leishmania.
Authors: Widmer G , Comeau A M , Furlong D B , Wirth D F , Patterson J L
Published: May 2006

We were interested in screening a series of isolates of the protozoan Leishmania for the presence of viruses. The experimental procedure we used was based on an enzymatic assay originally developed for viral RNA-dependent RNA polymerases. Simultaneously, total promastigote nucleic acid preparations were analyzed for the presence of viral genome and/or transcripts. Two isolates, both classified as L. braziliensis guyanensis, were found to be positive for RNA polymerase activity and to carry a large (6 kilobases) RNA species. The polymerase reaction products hybridized to the 6-kilobase RNA, believed to be the viral genome. In conjunction with electron microscopical observations these results indicate the presence of an RNA virus in these Leishmania isolates.
Template supercoiling during ATP-dependent DNA helix tracking: studies with simian virus 40 large tumor antigen.
Authors: Yang L , Jessee C B , Lau K , Zhang H , Liu L F
Published: May 2006

Incubation of topologically relaxed plasmid DNA with simian virus 40 (SV40) large tumor antigen (T antigen), ATP, and eubacterial DNA topoisomerase I resulted in the formation of highly positively supercoiled DNA. Eukaryotic DNA topoisomerase I could not substitute for eubacterial DNA topoisomerase 1 in this reaction. Furthermore, the addition of eukaryotic topoisomerase I to a preincubated reaction mixture containing both T antigen and eubacterial topoisomerase I caused rapid relaxation of the positively supercoiled DNA. These results suggest that SV40 T antigen can introduce topoisomerase-relaxable supercoils into DNA in a reaction coupled to ATP hydrolysis. We interpret the observed T antigen supercoiling reaction in terms of a recently proposed twin-supercoiled-domain model that describes the mechanics of DNA helix-tracking processes. According to this model positive and negative supercoils are generated ahead of and behind the moving SV40 T antigen, respectively. The preferential relaxation of negative supercoils by eubacterial DNA topoisomerase I explains the accumulation of positive supercoils in the DNA template. The supercoiling assay using DNA conformation-specific eubacterial DNA topoisomerase I may be of general use for the detection of ATP-dependent DNA helix-tracking proteins.
Photoaffinity labeling of indole-3-acetic acid-binding proteins in maize
Authors: Jones Alan M. , Venis Michael A.
Published: May 2006

The photoaffinity labeling agent 5-azidoindole-3-acetic acid, an analog of the endogenous plant hormone indole-3-acetic acid (an auxin), was used to identify indole-3-acetic acid-binding proteins in maize. Two peptides with subunit molecular masses of 24 and 22 kilodaltons are specifically labeled in a saturable manner. Both peptides are slightly acidic and behave as dimers under nondenaturing conditions. The possibility that one of these peptides is the auxin receptor that mediates cell elongation in maize is discussed.
Transient expression of the cholecystokinin gene in male germ cells and accumulation of the peptide in the acrosomal granule: possible role of cholecystokinin in fertilization.
Authors: Persson H , Rehfeld J F , Ericsson A , Schalling M , Pelto-Huikko M , Hökfelt T
Published: May 2006

Expression of the gene encoding the neurotransmitter/neuromodulator cholecystokinin (CCK) was demonstrated in testis of several different species. Two testicular CCK mRNA transcripts of different sizes were detected, and studies on the ontogeny of CCK gene expression indicated that the gene was expressed in male germ cells. In situ hybridization revealed CCK mRNA-expressing cells in the peripheral parts of the seminiferous tubules. Biochemical identification showed that the majority of prepro-CCK products in the testis represented pro-CCK. Immunofluorescence studies revealed CCK-like peptides primarily in spermatocytes and spermatids of mouse, rat, and monkey. Immuno electron microscopy of monkey testis demonstrated CCK immunoreactivity in the acrosomal granule of spermatids. Hence, an interesting possibility is that CCK peptides can be released during the acrosome reaction and thus may be of importance in the fertilization process.
Protein evolution on rugged landscapes.
Authors: Macken C A , Perelson A S
Published: May 2006

We analyze a mathematical model of protein evolution in which the evolutionary process is viewed as hill-climbing on a random fitness landscape. In studying the structure of such landscapes, we note that a large number of local optima exist, and we calculate the time and number of mutational changes until a protein gets trapped at a local optimum. Such a hill-climbing process may underlie the evolution of antibody molecules by somatic hypermutation.
Structure and coding properties of Bs1, a maize retrovirus-like transposon.
Authors: Jin Y K , Bennetzen J L
Published: May 2006

We have sequenced Bs1, an insertion element isolated from a null allele of the Adh1 locus encoding alcohol dehydrogenase in maize. The Bs1 element is 3203 base pairs (bp) in length, has 302-bp identical long terminal direct repeats (LTRs), and created a 5-bp flanking direct duplication of target Adh1 DNA upon insertion. The 5' LTR is followed by a canonical primer binding site with homology to the plant initiator methionyl-tRNA, and the 3' LTR is directly preceded by a polypurine stretch like that observed in retroviruses and retrotransposons. Bs1 encodes two overlapping open reading frames specifying peptides of 740 and 168 amino acids. The longer open reading frame specifies a peptide with amino acid homology to the protease and nucleic acid binding moiety of retroviruses and retrotransposons. The deduced amino acid sequence encoded by Bs1 lacks convincing homology to the polymerase (reverse transcriptase) encoded by retroposons, despite the fact that this polymerase-encoding domain is routinely the most conserved region of any such element. The sequence and relatively small size of Bs1 suggest that this element is a deleted retrotransposon that inserted into Adh1 with the aid of a reverse transcriptase function provided in trans. In vitro transcribed Bs1 complementary RNA was translated in vitro to produce both a protein of 81 kDa representing open reading frame 1 (ORF1) and one of the 95-kDa size predicted for the frame-shifted fusion of ORF1 and ORF2. As with many other retroposons, the efficiency of translational initiation at the AUG beginning ORF1 was not noticeably affected by the presence of one or more upstream, unproductive AUGs in the complementary RNA transcript.
Human beta satellite DNA: genomic organization and sequence definition of a class of highly repetitive tandem DNA.
Authors: Waye J S , Willard H F
Published: May 2006

We describe a class of human repetitive DNA, called beta satellite, that, at a most fundamental level, exists as tandem arrays of diverged approximately equal to 68-base-pair monomer repeat units. The monomer units are organized as distinct subsets, each characterized by a multimeric higher-order repeat unit that is tandemly reiterated and represents a recent unit of amplification. We have cloned, characterized, and determined the sequence of two beta satellite higher-order repeat units: one located on chromosome 9, the other on the acrocentric chromosomes (13, 14, 15, 21, and 22) and perhaps other sites in the genome. Analysis by pulsed-field gel electrophoresis reveals that these tandem arrays are localized in large domains (50-300 kilobase pairs) that are marked by restriction fragment length polymorphisms. In total, beta satellite sequences comprise several million base pairs of DNA in the human genome. Analysis of this DNA family should permit insights into the nature of chromosome-specific and nonspecific modes of satellite DNA evolution and provide useful tools for probing the molecular organization and concerted evolution of the acrocentric chromosomes.
Murine "viable motheaten" mutation reveals a gene critical to the development of both B and T lymphocytes.
Authors: Sidman C L , Marshall J D , Allen R D
Published: May 2006

In lethally irradiated normal mice reconstituted with both normal and autoimmune mutant viable motheaten (mev) bone marrow, the mev-derived B and T cells display aberrant behavior, while those derived from the normal bone marrow develop and function normally. The observed developmental abnormalities of mev B and T lymphocytes are therefore intrinsic to these cell types, rather than being determined by defective influences from the cells' environment. These data bring into question the in vivo significance of reported intercellular regulatory defects in motheaten (me) and mev mice and suggest that these mutations affect a gene whose product acts cell autonomously in the development of several hematopoietic cell lineages including B and T lymphocytes.
Mutually exclusive use of viral promoters in Epstein-Barr virus latently infected lymphocytes.
Authors: Woisetschlaeger M , Strominger J L , Speck S H
Published: May 2006

Of the eight viral antigens known to be expressed during Epstein-Barr virus latency, six are transcribed from a major rightward transcriptional unit, which gives rise to mRNAs containing common 5' exons. Analysis of cDNA clones has identified the use of two different promoters (Wp and Cp), located near the left-hand end of the viral genome, in generating these viral messages. Characterization of the activities of these two viral promoters in a number of Burkitt lymphoma and lymphoblastoid cell lines has revealed exclusive usage of only one of these promoters in all cell lines examined. Transfection of reporter constructs containing Wp and/or Cp linked to the bacterial chloramphenicol acetyltransferase gene into several different Epstein-Barr virus-infected cell lines generally supports a model in which the mutually exclusive use of Cp or Wp is determined by cellular factors and not by viral strain variation.
Differential proteolytic activation of factor VIII-von Willebrand factor complex by thrombin.
Authors: Hill-Eubanks D C , Parker C G , Lollar P
Published: May 2006

Blood coagulation factor VIII (fVIII) is a plasma protein that is decreased or absent in hemophilia A. It is isolated as a mixture of heterodimers that contain a variably sized heavy chain and a common light chain. Thrombin catalyzes the activation of fVIII in a reaction that is associated with cleavages in both types of chain. We isolated a serine protease from Bothrops jararacussu snake venom that catalyzes thrombin-like heavy-chain cleavage but not light-chain cleavage in porcine fVIII as judged by NaDodSO4/PAGE and N-terminal sequence analysis. Using a plasma-free assay of the ability of activated fVIII to function as a cofactor in the activation of factor X by factor IXa, we found that fVIII is activated by the venom enzyme. The venom enzyme-activated fVIII was isolated in stable form by cation-exchange HPLC. von Willebrand factor inhibited venom enzyme-activated fVIII but not thrombin-activated fVIII. These results suggest that the binding of fVIII to von Willebrand factor depends on the presence of an intact light chain and that activated fVIII must dissociate from von Willebrand factor to exert its cofactor effect. Thus, proteolytic activation of fVIII-von Willebrand factor complex appears to be differentially regulated by light-chain cleavage to dissociate the complex and heavy-chain cleavage to activate the cofactor function.
Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically.
Authors: Sarai A , Takeda Y
Published: May 2006

Results of systematic base-substitution experiments suggest that the lambda repressor dimer, made of identical subunits, recognizes the "pseudo(2-fold)symmetric" operator sequence asymmetrically. Base substitutions within the consensus half of the operator affect binding more than base substitutions within the nonconsensus half of the operator. Furthermore, changing the nonconsensus base pairs to the consensus base pairs does not increase, but decreases, binding. Evidently, the two subunits of the lambda repressor dimer bind to the two halves of the operator differently. This is consistent with the recently determined crystal structure of the complex, which shows that the relative positioning of the amino acids to the DNA bases are slightly different in the two halves of the operator. The sequence-specific interactions indicated by the systematic base-substitution experiments correlate well with the locations of the specific contacts found in the complex. Thus, the amino acids of lambda repressor, mainly of alpha 3-helix and the N-terminus arm, seem to directly read-out the DNA sequence by forming specific hydrogen bonds and hydrophobic contacts to the DNA bases. The observed asymmetric recognition suggests that no recognition code governs amino acids and DNA bases in protein-DNA interactions.
Magainins and the disruption of membrane-linked free-energy transduction.
Authors: Westerhoff H V , Juretić D , Hendler R W , Zasloff M
Published: May 2006

Magainins, a family of positively charged peptides, are partly if not wholly responsible for antimicrobial activity in skin extracts of Xenopus laevis. We report here that members of the magainin family--i.e., the 21-amino acid peptide PGLa and the 23-amino acid peptide magainin 2 amide (PGSa)--dissipate the electric potential across various energy-transducing membranes and thus uncouple respiration from other free-energy-requiring processes. We propose that this is a likely mechanism for the antimicrobial effects of these compounds.
Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes.
Authors: Gogarten J P , Kibak H , Dittrich P , Taiz L , Bowman E J , Bowman B J , Manolson M F , Poole R J , Date T , Oshima T , Konishi J , Denda K , Yoshida M
Published: May 2006

Active transport across the vacuolar components of the eukaryotic endomembrane system is energized by a specific vacuolar H+-ATPase. The amino acid sequences of the 70- and 60-kDa subunits of the vacuolar H+-ATPase are approximately equal to 25% identical to the beta and alpha subunits, respectively, of the eubacterial-type F0F1-ATPases. We now report that the same vacuolar H+-ATPase subunits are approximately equal to 50% identical to the alpha and beta subunits, respectively, of the sulfur-metabolizing Sulfolobus acidocaldarius, an archaebacterium (Archaeobacterium). Moreover, the homologue of an 88-amino acid stretch near the amino-terminal end of the 70-kDa subunit is absent from the F0F1-ATPase beta subunit but is present in the alpha subunit of Sulfolobus. Since the two types of subunits (alpha and beta subunits; 60- and 70-kDa subunits) are homologous to each other, they must have arisen by a gene duplication that occurred prior to the last common ancestor of the eubacteria, eukaryotes, and Sulfolobus. Thus, the phylogenetic tree of the subunits can be rooted at the site where the gene duplication occurred. The inferred evolutionary tree contains two main branches: a eubacterial branch and an eocyte branch that gave rise to Sulfolobus and the eukaryotic host cell. The implication is that the vacuolar H+-ATPase of eukaryotes arose by the internalization of the plasma membrane H+-ATPase of an archaebacterial-like ancestral cell.
Selective changes in expression of HLA class I polymorphic determinants in human solid tumors.
Authors: Natali P G , Nicotra M R , Bigotti A , Venturo I , Marcenaro L , Giacomini P , Russo C
Published: May 2006

Analysis of surgical biopsies with monoclonal antibodies (mAbs) to framework determinants of major histocompatibility complex class I antigens has shown that malignant transformation is frequently associated with a marked loss of these cell surface molecules. The present study sought to determine whether more selective losses of major histocompatibility complex class I expression occur. Multiple specimens from 13 different types of primary and metastatic tumors were tested utilizing mAb BB7.2, which recognizes a polymorphic HLA-A2 epitope. In each case, expression of HLA-A,B,C molecules was determined by testing with mAb W6/32 directed to a framework HLA class I determinant. We have found that in HLA-A2-positive patients (identified by reactivity of their normal tissues with mAb BB7.2), HLA-A2 products are not detectable or are reduced in their expression in 70-80% of endometrial, colorectal, mammary, and renal tumors; in 40-60% of soft-tissue, skin, ovary, urinary bladder, prostate, and stomach tumors; and in 25-30% of melanomas and lung carcinomas tested. All tumors expressed the framework HLA-A,B,C determinant. The HLA-A2 epitope recognized by mAb BB7.2 is located in a portion of the HLA-A2 molecule postulated to react with the T-cell receptor. Immune surveillance to tumors is thought to depend on cytotoxic T cells, which require corecognition of polymorphic HLA class I epitopes, and on natural killer cells, which are, on the contrary, activated by the absence of HLA class I antigens. The selective loss of an HLA class I polymorphic epitope shown in this study may explain the mechanism by which tumor cells escape both T-cell recognition and natural killer cell surveillance.
Changes in CD45 isoform expression accompany antigen-induced murine T-cell activation.
Authors: Birkeland M L , Johnson P , Trowbridge I S , Puré E
Published: May 2006

Leukocytes express a family of plasma membrane proteins called CD45 or the leukocyte common antigen. Isoforms of various molecular masses, 180-240 kDa, are produced by alternative splicing and usage of three exons, named A, B, and C, that encode the N-terminal portion of the external domain. By using monoclonal antibodies that precipitate B exon-dependent and B exon-independent isoforms we find that both murine CD4+ and murine CD8+ T cells selectively down-regulate the B exon-dependent forms of CD45 during an immune response. This change was monitored by using fluorescence-activated cell sorter (FACS) analysis and immunoprecipitation from surface radioiodinated and metabolically labeled cells. The loss of the 190-kDa B exon-dependent isoform during T-cell activation is accompanied by an increased production of a 180-kDa form, which does not contain the B exon-encoded sequence. This accounts for our observation that the overall expression of CD45, as assessed by FACS analysis, does not change.
Recombinant tumor necrosis factor alpha and interleukin 1 alpha increase expression of c-abl protooncogene mRNA in cultured human marrow stromal cells.
Authors: Andrews D F , Nemunaitis J J , Singer J W
Published: May 2006

Analysis of protooncogene RNA expression in marrow stromal cells from long-term marrow culture demonstrated high levels of c-abl 5-, 6-, and 7-kilobase (kb) RNA transcripts. In experiments on three independently derived simian virus 40-transformed marrow stromal cell lines, the expression of these c-abl transcripts was further increased in response to recombinant tumor necrosis factor alpha (1000 units/ml) and interleukin 1 alpha (10 units/ml). Although lymphocyte-conditioned medium predominantly up-regulated the 5-kb transcript, interleukin 1 alpha primarily affected the 6-kb transcript. The up-regulation of the 5-kb c-abl message correlated with up-regulation of the granulocyte/macrophage colony-stimulating factor transcript and down-regulation of procollagen I transcripts in transformed cells. These data suggest that c-abl plays roles in the regulation of extracellular matrix expression and in the regulation of hematopoietic growth factors by stromal cells.
Nucleotide-sequence-specific de novo methylation in a somatic murine cell line.
Authors: Szyf M , Schimmer B P , Seidman J G
Published: May 2006

DNA fragments encoding the mouse steroid 21-hydroxylase (C21 or Cyp21A1) gene are de novo methylated when introduced into the mouse adrenocortical tumor cell line Y1 by DNA-mediated gene transfer. Although CCGG sequences within the C21 gene are de novo methylated, CCGG sites within flanking vector sequences, other mammalian gene sequences driven by the C21 promoter, and the neomycin-resistance gene, which was cotransfected with the C21 gene, do not become methylated. At least two separate signals for de novo methylation are encoded within the gene since three fragments derived from the C21 gene were methylated de novo. Specific de novo methylation of C21-derived sequences does not occur in L cells or Y1 kin8 cells; this suggests that the cellular factors needed for de novo methylation of the C21 gene are not ubiquitous. Most DNA sequences are not de novo methylated when introduced into somatic cells and DNA sequences other than the C21 gene are not de novo methylated when introduced into Y1 cells. Several groups have suggested that de novo methylation occurs in early embryonic cells and that somatic cells strictly maintain their methylation pattern by a semiconservative methyltransferase. Our results suggest that de novo methylation of specific nucleotide sequences can occur in some mammalian somatic cells.
Design and creation of a Ca2+ binding site in human lysozyme to enhance structural stability.
Authors: Kuroki R , Taniyama Y , Seko C , Nakamura H , Kikuchi M , Ikehara M
Published: May 2006

A Ca2+ binding site like an EF-hand motif was designed and created in human lysozyme by replacing both Gln-86 and Ala-92 with aspartic acids by site-directed mutagenesis. The mutant human lysozyme (D86/92-lysozyme) was expressed and secreted by yeast. One Ca2+ was found to bind one molecule of the purified protein with the binding constant 5.0 x 10(6) M-1. The enzymatic activity of holo-D86/92-lysozyme against glycol chitin at 40 degrees C was 2-fold higher than that of the native lysozyme. Maximal activity of the holo-D86/92-lysozyme was observed at 80 degrees C, where its relative activity normalized to the value at 40 degrees C was 6-fold and 17-fold higher than those of the native and apoenzymes, respectively. The activities of the native lysozyme and apo-D86/92-lysozyme were maximum at 65 degrees C-70 degrees C. Moreover, D86/92-lysozyme was more stable against protease digestion than the native lysozyme. These results indicate that the creation of the calcium binding site like an EF-hand motif in the human lysozyme enhances its structural stability.